Comparing metabolomic and transcriptomic data.

1 Comparing metabolomic and transcriptomic data

One of the recent discussions surrounding the TMRC3 data is centered on a series of metabolomic experiments. I have not yet spent the time to truly understand the experiment performed, I am hoping to use the process of writing this document to amend that. In addition, this document will hopefully provide some of the pieces of inquiry useful for informing the overall discussion.

1.1 The metabolomic data

This portion of the data is coming from Alejandro’s paper: “Pharmacometabolomics of Meglumine Antimoniate in Patients With Cutaneous Leishmaniasis.” I therefore am dropping a copy of this paper in the ‘downloaded_data’ directory and reading it before I make any more assumptions.

2 Collecting the transcriptomic results

There is one super-important caveat when collecting the transcriptomic data: the TMRC3 data includes two different drug regimes with apparently two very different effects on the person’s metabolism. As a result, I cannot use the set of all samples, but must limit it to the samples which used glucantine and not miltefosine.

In our most recent conversation, the focus shifted to two primary contrasts performed in the data:

1. The comparison of visit 3 / visit 1 in monocytes treated with glucantine.
2. The comparison of visit 3 / visit 1 in biopsies treated with glucantine.

I therefore copied the DE table data structures to the rda/ directory and will do some simple tests on it.

2.0.1 Collecting monocytes

monocyte <- new.env()
load(file = "rda/visit_monocyte_gluc_table-v202011.rda", envir = monocyte)
monocyte <- monocyte[["visit_monocyte_gluc_table"]]

monocyte_topn <- extract_significant_genes(monocyte, n = 100, according_to = "deseq")

## Getting the top and bottom 100 genes.
## Getting the top and bottom 100 genes.
## Getting the top and bottom 100 genes.

monocyte_v2v1_up <- monocyte_topn[["deseq"]][["ups"]][["v2v1"]]
monocyte_v2v1_down <- monocyte_topn[["deseq"]][["downs"]][["v2v1"]]
monocyte_v3v1_up <- monocyte_topn[["deseq"]][["ups"]][["v3v1"]]
monocyte_v3v1_down <- monocyte_topn[["deseq"]][["downs"]][["v3v1"]]

2.0.2 Collecting data biopsies

biopsy <- new.env()
load(file = "rda/visit_biopsy_gluc_table-v202011.rda", envir = biopsy)
biopsy <- biopsy[["visit_biopsy_gluc_table"]]

biopsy_topn <- extract_significant_genes(biopsy, according_to = "deseq")
biopsy_v2v1_up <- biopsy_topn[["deseq"]][["ups"]][["v2v1"]]
dim(biopsy_v2v1_up)

## [1] 189  58

biopsy_v2v1_down <- biopsy_topn[["deseq"]][["downs"]][["v2v1"]]
dim(biopsy_v2v1_down)

## [1] 275  58

biopsy_v3v1_up <- biopsy_topn[["deseq"]][["ups"]][["v3v1"]]
dim(biopsy_v3v1_up)

## [1] 1143   58

biopsy_v3v1_down <- biopsy_topn[["deseq"]][["downs"]][["v3v1"]]
dim(biopsy_v3v1_down)

## [1] 722  58

2.1 GSEA of visits

2.1.1 Monocytes

monocyte_v2v1_gpup <- simple_gprofiler(monocyte_v2v1_up)

## Performing gProfiler GO search of 100 genes against hsapiens.

## GO search found 55 hits.

## Performing gProfiler KEGG search of 100 genes against hsapiens.

## KEGG search found 9 hits.

## Performing gProfiler REAC search of 100 genes against hsapiens.

## REAC search found 8 hits.

## Performing gProfiler MI search of 100 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 100 genes against hsapiens.

## TF search found 0 hits.

## Performing gProfiler CORUM search of 100 genes against hsapiens.

## CORUM search found 0 hits.

## Performing gProfiler HP search of 100 genes against hsapiens.

## HP search found 0 hits.

monocyte_v2v1_gpup[["pvalue_plots"]][["bpp_plot_over"]]

monocyte_v2v1_gpup[["pvalue_plots"]][["mfp_plot_over"]]

monocyte_v2v1_gpup[["pvalue_plots"]][["kegg_plot_over"]]

monocyte_v2v1_gpdown <- simple_gprofiler(monocyte_v2v1_down)

## Performing gProfiler GO search of 100 genes against hsapiens.

## GO search found 5 hits.

## Performing gProfiler KEGG search of 100 genes against hsapiens.

## KEGG search found 3 hits.

## Performing gProfiler REAC search of 100 genes against hsapiens.

## REAC search found 0 hits.

## Performing gProfiler MI search of 100 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 100 genes against hsapiens.

## TF search found 2 hits.

## Performing gProfiler CORUM search of 100 genes against hsapiens.

## CORUM search found 1 hits.

## Performing gProfiler HP search of 100 genes against hsapiens.

## HP search found 7 hits.

monocyte_v2v1_gpdown[["pvalue_plots"]][["bpp_plot_over"]]

monocyte_v2v1_gpdown[["pvalue_plots"]][["mfp_plot_over"]]

monocyte_v2v1_gpdown[["pvalue_plots"]][["kegg_plot_over"]]

monocyte_v3v1_gpup <- simple_gprofiler(monocyte_v3v1_up)

## Performing gProfiler GO search of 100 genes against hsapiens.

## GO search found 52 hits.

## Performing gProfiler KEGG search of 100 genes against hsapiens.

## KEGG search found 2 hits.

## Performing gProfiler REAC search of 100 genes against hsapiens.

## REAC search found 1 hits.

## Performing gProfiler MI search of 100 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 100 genes against hsapiens.

## TF search found 2 hits.

## Performing gProfiler CORUM search of 100 genes against hsapiens.

## CORUM search found 0 hits.

## Performing gProfiler HP search of 100 genes against hsapiens.

## HP search found 0 hits.

monocyte_v3v1_gpup[["pvalue_plots"]][["bpp_plot_over"]]

monocyte_v3v1_gpup[["pvalue_plots"]][["mfp_plot_over"]]

monocyte_v3v1_gpup[["pvalue_plots"]][["kegg_plot_over"]]

monocyte_v3v1_gpdown <- simple_gprofiler(monocyte_v3v1_down)

## Performing gProfiler GO search of 100 genes against hsapiens.

## GO search found 28 hits.

## Performing gProfiler KEGG search of 100 genes against hsapiens.

## KEGG search found 4 hits.

## Performing gProfiler REAC search of 100 genes against hsapiens.

## REAC search found 3 hits.

## Performing gProfiler MI search of 100 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 100 genes against hsapiens.

## TF search found 1 hits.

## Performing gProfiler CORUM search of 100 genes against hsapiens.

## CORUM search found 1 hits.

## Performing gProfiler HP search of 100 genes against hsapiens.

## HP search found 5 hits.

monocyte_v3v1_gpdown[["pvalue_plots"]][["bpp_plot_over"]]

monocyte_v3v1_gpdown[["pvalue_plots"]][["mfp_plot_over"]]

monocyte_v3v1_gpdown[["pvalue_plots"]][["kegg_plot_over"]]

2.1.2 Biopsys

biopsy_v2v1_gpup <- simple_gprofiler(biopsy_v2v1_up)

## Performing gProfiler GO search of 189 genes against hsapiens.

## GO search found 71 hits.

## Performing gProfiler KEGG search of 189 genes against hsapiens.

## KEGG search found 3 hits.

## Performing gProfiler REAC search of 189 genes against hsapiens.

## REAC search found 9 hits.

## Performing gProfiler MI search of 189 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 189 genes against hsapiens.

## TF search found 0 hits.

## Performing gProfiler CORUM search of 189 genes against hsapiens.

## CORUM search found 1 hits.

## Performing gProfiler HP search of 189 genes against hsapiens.

## HP search found 1 hits.

biopsy_v2v1_gpup[["pvalue_plots"]][["bpp_plot_over"]]

biopsy_v2v1_gpup[["pvalue_plots"]][["mfp_plot_over"]]

biopsy_v2v1_gpup[["pvalue_plots"]][["kegg_plot_over"]]

biopsy_v2v1_gpdown <- simple_gprofiler(biopsy_v2v1_down)

## Performing gProfiler GO search of 275 genes against hsapiens.

## GO search found 366 hits.

## Performing gProfiler KEGG search of 275 genes against hsapiens.

## KEGG search found 23 hits.

## Performing gProfiler REAC search of 275 genes against hsapiens.

## REAC search found 20 hits.

## Performing gProfiler MI search of 275 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 275 genes against hsapiens.

## TF search found 31 hits.

## Performing gProfiler CORUM search of 275 genes against hsapiens.

## CORUM search found 0 hits.

## Performing gProfiler HP search of 275 genes against hsapiens.

## HP search found 4 hits.

biopsy_v2v1_gpdown[["pvalue_plots"]][["bpp_plot_over"]]

biopsy_v2v1_gpdown[["pvalue_plots"]][["mfp_plot_over"]]

biopsy_v2v1_gpdown[["pvalue_plots"]][["kegg_plot_over"]]

biopsy_v3v1_gpup <- simple_gprofiler(
    biopsy_v3v1_up,
    excel = glue::glue("excel/v3v1_up_gprofiler-v{ver}.xlsx"))

## Performing gProfiler GO search of 1143 genes against hsapiens.

## GO search found 227 hits.

## Performing gProfiler KEGG search of 1143 genes against hsapiens.

## KEGG search found 15 hits.

## Performing gProfiler REAC search of 1143 genes against hsapiens.

## REAC search found 19 hits.

## Performing gProfiler MI search of 1143 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 1143 genes against hsapiens.

## TF search found 153 hits.

## Performing gProfiler CORUM search of 1143 genes against hsapiens.

## CORUM search found 1 hits.

## Performing gProfiler HP search of 1143 genes against hsapiens.

## HP search found 31 hits.

## Writing data to: excel/v3v1_up_gprofiler-v20220119.xlsx.

## Finished writing data.

biopsy_v3v1_gpup[["pvalue_plots"]][["bpp_plot_over"]]

biopsy_v3v1_gpup[["pvalue_plots"]][["mfp_plot_over"]]

biopsy_v3v1_gpup[["pvalue_plots"]][["kegg_plot_over"]]

biopsy_v3v1_gpup[["pvalue_plots"]][["reactome_plot_over"]]

biopsy_v3v1_gpdown <- simple_gprofiler(
    biopsy_v3v1_down,
    excel = glue::glue("excel/v3v1_down_gprofiler-v{ver}.xlsx"))

## Performing gProfiler GO search of 722 genes against hsapiens.

## GO search found 764 hits.

## Performing gProfiler KEGG search of 722 genes against hsapiens.

## KEGG search found 54 hits.

## Performing gProfiler REAC search of 722 genes against hsapiens.

## REAC search found 65 hits.

## Performing gProfiler MI search of 722 genes against hsapiens.

## MI search found 0 hits.

## Performing gProfiler TF search of 722 genes against hsapiens.

## TF search found 132 hits.

## Performing gProfiler CORUM search of 722 genes against hsapiens.

## CORUM search found 9 hits.

## Performing gProfiler HP search of 722 genes against hsapiens.

## HP search found 20 hits.

## Writing data to: excel/v3v1_down_gprofiler-v20220119.xlsx.

## Finished writing data.

biopsy_v3v1_gpdown[["pvalue_plots"]][["bpp_plot_over"]]

biopsy_v3v1_gpdown[["pvalue_plots"]][["mfp_plot_over"]]

biopsy_v3v1_gpdown[["pvalue_plots"]][["kegg_plot_over"]]

3 GSVA of the upstream data sets

3.1 Monocytes

3.2 Biopsies

4 KEGG Mapping and Cross Referencing

In order to color the various KEGG path diagrams, we will need to make some bridges across the various databases, though I think the bridges will need to be less interesting than they were when we thought it was L. panamensis.

The things we will need (I think):

1. Mapping from the Ensembl IDs to NCBI IDs (load_biomart), and the KEGG IDs to NCBI (load_kegg).
2. Table of kegg and gene IDs.
3. Set of pathways of interest.

4.1 Starter set

Lets make it easy on ourselves and just color some KEGG pictures with the observed genes from the biopsy up/down.

updown_genes <- rbind(biopsy_v3v1_up, biopsy_v3v1_down)

wanted_columns <- c("ensembl_gene_id", "ensembl_gene_id_version",
                    "entrez_trans_name", "entrezgene_description",
                    "entrezgene_accession", "entrezgene_id")
hs_annot <- load_biomart_annotations(archive = FALSE, gene_requests = wanted_columns,
                                     include_lengths = FALSE, overwrite = TRUE)[["annotation"]]

## Using mart: ENSEMBL_MART_ENSEMBL from host: useast.ensembl.org.

## Successfully connected to the hsapiens_gene_ensembl database.

## Some attributes in your request list were not in the ensembl database.

## Finished downloading ensembl gene annotations.

## drop_haplotypes is TRUE, but there is no chromosome information.

## Saving annotations to hsapiens_biomart_annotations.rda.

## Finished save().

kegg_annot <- load_kegg_annotations(abbreviation = "hsa")

## hs_annot says that hsa:7105 is tetraspannin.6, how about kegg?
test_id <- "7105"
test_hsa_idx <- hs_annot[["entrezgene_id"]] == test_id
head(hs_annot[test_hsa_idx, ], n = 1)

##                 ensembl_gene_id ensembl_gene_id_version entrezgene_description
## ENSG00000000003 ENSG00000000003      ENSG00000000003.15          tetraspanin 6
##                 entrezgene_accession entrezgene_id
## ENSG00000000003               TSPAN6          7105

test_kegg_idx <- kegg_annot[["kegg_geneid"]] == paste0("hsa:", test_id)
kegg_annot[test_kegg_idx, ]

##        GID ncbi_geneid ncbi_proteinid uniprotid pathways kegg_geneid
## X7105 7105        7105      NP_003261    O43657             hsa:7105

interesting_stuff <- merge(updown_genes, hs_annot,
                           by.x = "ensemblgeneid", by.y = "ensembl_gene_id", all.x = TRUE)
dim(updown_genes)

## [1] 1865   58

dim(interesting_stuff)

## [1] 1878   62

## So, there appear to be a few duplicates, that should be ok.
interesting_stuff[["kegg_prefix_id"]] <- paste0("hsa:", interesting_stuff[["entrezgene_id"]])
## interesting_stuff <- merge(interesting_stuff, kegg_annot, by.x = "temp_id", by.y = "kegg_geneid")
## Hey doofus, kegg uses 'hsa:', followed by the NCBI entrez gene ID,
## I don't need to cross reference the darn kegg IDs at all.
## well, ok, lets see if we get any fun colored paths...

pathview_input <- interesting_stuff
testing <- simple_pathview(gene_input = pathview_input, species = "hsa",
                           fc_column = "deseq_logfc",
                           id_column = "entrezgene_id")

## Here are some path gene examples: gn:T01001, 10327, 124, 125, 126, 127

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 9 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00010._colored.png

## 1/345: Finished glycolysis_/_gluconeogenesis id: hsa00010 with 22.86% genes mapped(7 unique).

## Here are some path gene examples: gn:T01001, 1431, 1737, 1738, 1743, 2271

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 1 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00020._colored.png

## 2/345: Finished citrate_cycle_(tca_cycle) id: hsa00020 with 4.545% genes mapped(1 unique).

## Here are some path gene examples: gn:T01001, 132158, 2203, 221823, 226, 229

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 2 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00030._colored.png

## 3/345: Finished pentose_phosphate_pathway id: hsa00030 with 7.692% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00040._colored.png

## 4/345: Finished pentose_and_glucuronate_interconversions id: hsa00040 with 14.29% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00051._colored.png

## 5/345: Finished fructose_and_mannose_metabolism id: hsa00051 with 20% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00052._colored.png

## 6/345: Finished galactose_metabolism id: hsa00052 with 8.333% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00053._colored.png

## 7/345: Finished ascorbate_and_aldarate_metabolism id: hsa00053 with 37.5% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00061._colored.png

## 8/345: Finished fatty_acid_biosynthesis id: hsa00061 with 3.297% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00062._colored.png

## Info: some node width is different from others, and hence adjusted!

## 9/345: Finished fatty_acid_elongation id: hsa00062 with 5.128% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00071._colored.png

## 10/345: Finished fatty_acid_degradation id: hsa00071 with 6.349% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00100._colored.png

## 11/345: Finished steroid_biosynthesis id: hsa00100 with 45% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00120._colored.png

## 12/345: Finished primary_bile_acid_biosynthesis id: hsa00120 with 15.22% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00130._colored.png

## 13/345: Finished ubiquinone_and_other_terpenoid-quinone_biosynthesis id: hsa00130 with 14.29% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00140._colored.png

## 14/345: Finished steroid_hormone_biosynthesis id: hsa00140 with 25.47% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00190._colored.png

## Info: some node width is different from others, and hence adjusted!
## Info: some node width is different from others, and hence adjusted!

## 15/345: Finished oxidative_phosphorylation id: hsa00190 with 4.425% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00220._colored.png

## 16/345: Finished arginine_biosynthesis id: hsa00220 with 38.46% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00230._colored.png

## 17/345: Finished purine_metabolism id: hsa00230 with 15.53% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00232._colored.png

## 18/345: Finished caffeine_metabolism id: hsa00232 with 44.44% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00240._colored.png

## 19/345: Finished pyrimidine_metabolism id: hsa00240 with 21.21% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00250._colored.png

## 20/345: Finished alanine,_aspartate_and_glutamate_metabolism id: hsa00250 with 18.18% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00260._colored.png

## 21/345: Finished glycine,_serine_and_threonine_metabolism id: hsa00260 with 30.56% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00270._colored.png

## 22/345: Finished cysteine_and_methionine_metabolism id: hsa00270 with 13.16% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00280._colored.png

## 23/345: Finished valine,_leucine_and_isoleucine_degradation id: hsa00280 with 6% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00290._colored.png

## 24/345: Finished valine,_leucine_and_isoleucine_biosynthesis id: hsa00290 with 25% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00310._colored.png

## 25/345: Finished lysine_degradation id: hsa00310 with 20.83% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00330._colored.png

## 26/345: Finished arginine_and_proline_metabolism id: hsa00330 with 30.77% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00340._colored.png

## 27/345: Finished histidine_metabolism id: hsa00340 with 31.25% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00350._colored.png

## 28/345: Finished tyrosine_metabolism id: hsa00350 with 56.52% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00360._colored.png

## 29/345: Finished phenylalanine_metabolism id: hsa00360 with 40% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00380._colored.png

## 30/345: Finished tryptophan_metabolism id: hsa00380 with 41.86% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00400._colored.png

## 31/345: Finished phenylalanine,_tyrosine_and_tryptophan_biosynthesis id: hsa00400 with 28.57% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00410._colored.png

## 32/345: Finished beta-alanine_metabolism id: hsa00410 with 13.04% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00430._colored.png

## 33/345: Finished taurine_and_hypotaurine_metabolism id: hsa00430 with 25% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00440._colored.png

## 34/345: Finished phosphonate_and_phosphinate_metabolism id: hsa00440 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00450._colored.png

## 35/345: Finished selenocompound_metabolism id: hsa00450 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00470._colored.png

## 36/345: Finished d-amino_acid_metabolism id: hsa00470 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00480._colored.png

## 37/345: Finished glutathione_metabolism id: hsa00480 with 41.38% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00500._colored.png

## Info: some node width is different from others, and hence adjusted!

## 38/345: Finished starch_and_sucrose_metabolism id: hsa00500 with 16% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00510._colored.png

## 39/345: Finished n-glycan_biosynthesis id: hsa00510 with 5.128% genes mapped(2 unique).

## Warning: Number of mappable nodes is below 3, hsa00511 skipped!

## Warning in simple_pathview(gene_input = pathview_input, species = "hsa", : There
## was a failure for: hsa00511.

## 40/345: Finished other_glycan_degradation id: hsa00511 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00512._colored.png

## 41/345: Finished mucin_type_o-glycan_biosynthesis id: hsa00512 with 7.692% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00513._colored.png

## 42/345: Finished various_types_of_n-glycan_biosynthesis id: hsa00513 with 3.333% genes mapped(1 unique).

## Warning: Number of mappable nodes is below 3, hsa00514 skipped!

## Warning in simple_pathview(gene_input = pathview_input, species = "hsa", : There
## was a failure for: hsa00514.

## 43/345: Finished other_types_of_o-glycan_biosynthesis id: hsa00514 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00515._colored.png

## 44/345: Finished mannose_type_o-glycan_biosynthesis id: hsa00515 with 13.64% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00520._colored.png

## 45/345: Finished amino_sugar_and_nucleotide_sugar_metabolism id: hsa00520 with 18.37% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00524._colored.png

## 46/345: Finished neomycin,_kanamycin_and_gentamicin_biosynthesis id: hsa00524 with 50% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00531._colored.png

## 47/345: Finished glycosaminoglycan_degradation id: hsa00531 with 19.05% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00532._colored.png

## 48/345: Finished glycosaminoglycan_biosynthesis_-_chondroitin_sulfate_/_dermatan_sulfate id: hsa00532 with 5.263% genes mapped(1 unique).

## Warning: Number of mappable nodes is below 3, hsa00533 skipped!

## Warning in simple_pathview(gene_input = pathview_input, species = "hsa", : There
## was a failure for: hsa00533.

## 49/345: Finished glycosaminoglycan_biosynthesis_-_keratan_sulfate id: hsa00533 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00534._colored.png

## 50/345: Finished glycosaminoglycan_biosynthesis_-_heparan_sulfate_/_heparin id: hsa00534 with 13.04% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00561._colored.png

## 51/345: Finished glycerolipid_metabolism id: hsa00561 with 52.63% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00562._colored.png

## 52/345: Finished inositol_phosphate_metabolism id: hsa00562 with 7.692% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00563._colored.png

## 53/345: Finished glycosylphosphatidylinositol_(gpi)-anchor_biosynthesis id: hsa00563 with 3.846% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00564._colored.png

## 54/345: Finished glycerophospholipid_metabolism id: hsa00564 with 21.57% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00565._colored.png

## 55/345: Finished ether_lipid_metabolism id: hsa00565 with 15% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00590._colored.png

## 56/345: Finished arachidonic_acid_metabolism id: hsa00590 with 57.14% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00591._colored.png

## 57/345: Finished linoleic_acid_metabolism id: hsa00591 with 33.33% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00592._colored.png

## 58/345: Finished alpha-linolenic_acid_metabolism id: hsa00592 with 11.11% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00600._colored.png

## 59/345: Finished sphingolipid_metabolism id: hsa00600 with 36.11% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00601._colored.png

## 60/345: Finished glycosphingolipid_biosynthesis_-_lacto_and_neolacto_series id: hsa00601 with 5.333% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00603._colored.png

## 61/345: Finished glycosphingolipid_biosynthesis_-_globo_and_isoglobo_series id: hsa00603 with 5.882% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00604._colored.png

## 62/345: Finished glycosphingolipid_biosynthesis_-_ganglio_series id: hsa00604 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00620._colored.png

## 63/345: Finished pyruvate_metabolism id: hsa00620 with 20% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00630._colored.png

## 64/345: Finished glyoxylate_and_dicarboxylate_metabolism id: hsa00630 with 8.333% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00640._colored.png

## 65/345: Finished propanoate_metabolism id: hsa00640 with 4.167% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00650._colored.png

## 66/345: Finished butanoate_metabolism id: hsa00650 with 21.43% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00670._colored.png

## 67/345: Finished one_carbon_pool_by_folate id: hsa00670 with 4.545% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00730._colored.png

## 68/345: Finished thiamine_metabolism id: hsa00730 with 28.57% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00740._colored.png

## 69/345: Finished riboflavin_metabolism id: hsa00740 with 40% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00750._colored.png

## 70/345: Finished vitamin_b6_metabolism id: hsa00750 with 8.333% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00760._colored.png

## 71/345: Finished nicotinate_and_nicotinamide_metabolism id: hsa00760 with 37.04% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00770._colored.png

## 72/345: Finished pantothenate_and_coa_biosynthesis id: hsa00770 with 31.25% genes mapped(3 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00780._colored.png

## 73/345: Finished biotin_metabolism id: hsa00780 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00785._colored.png

## 74/345: Finished lipoic_acid_metabolism id: hsa00785 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00790._colored.png

## 75/345: Finished folate_biosynthesis id: hsa00790 with 20.59% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00830._colored.png

## 76/345: Finished retinol_metabolism id: hsa00830 with 35.14% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00860._colored.png

## 77/345: Finished porphyrin_metabolism id: hsa00860 with 4.167% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00900._colored.png

## 78/345: Finished terpenoid_backbone_biosynthesis id: hsa00900 with 11.11% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00910._colored.png

## 79/345: Finished nitrogen_metabolism id: hsa00910 with 75% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00920._colored.png

## 80/345: Finished sulfur_metabolism id: hsa00920 with 30% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00970._colored.png

## 81/345: Finished aminoacyl-trna_biosynthesis id: hsa00970 with 6.522% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00980._colored.png

## 82/345: Finished metabolism_of_xenobiotics_by_cytochrome_p450 id: hsa00980 with 27.91% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00982._colored.png

## 83/345: Finished drug_metabolism_-_cytochrome_p450 id: hsa00982 with 18.03% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00983._colored.png

## 84/345: Finished drug_metabolism_-_other_enzymes id: hsa00983 with 19.51% genes mapped(7 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01040._colored.png

## 85/345: Finished biosynthesis_of_unsaturated_fatty_acids id: hsa01040 with 0% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01100._colored.png

## 86/345: Finished metabolic_pathways id: hsa01100 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01200._colored.png

## Info: some node width is different from others, and hence adjusted!

## 87/345: Finished carbon_metabolism id: hsa01200 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01210._colored.png

## 88/345: Finished 2-oxocarboxylic_acid_metabolism id: hsa01210 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01212._colored.png

## Info: some node width is different from others, and hence adjusted!

## 89/345: Finished fatty_acid_metabolism id: hsa01212 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01230._colored.png

## 90/345: Finished biosynthesis_of_amino_acids id: hsa01230 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01240._colored.png

## 91/345: Finished biosynthesis_of_cofactors id: hsa01240 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01250._colored.png

## 92/345: Finished biosynthesis_of_nucleotide_sugars id: hsa01250 with NaN% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01521._colored.png

## 93/345: Finished egfr_tyrosine_kinase_inhibitor_resistance id: hsa01521 with 20.34% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01522._colored.png

## 94/345: Finished endocrine_resistance id: hsa01522 with 10% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01523._colored.png

## 95/345: Finished antifolate_resistance id: hsa01523 with 19.23% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01524._colored.png

## 96/345: Finished platinum_drug_resistance id: hsa01524 with 8.511% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa02010._colored.png

## 97/345: Finished abc_transporters id: hsa02010 with 24.44% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03008._colored.png

## 98/345: Finished ribosome_biogenesis_in_eukaryotes id: hsa03008 with 1.613% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03010._colored.png

## 99/345: Finished ribosome id: hsa03010 with 0.8065% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03013._colored.png

## 100/345: Finished nucleocytoplasmic_transport id: hsa03013 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03015._colored.png

## 101/345: Finished mrna_surveillance_pathway id: hsa03015 with 3.509% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03018._colored.png

## 102/345: Finished rna_degradation id: hsa03018 with 1.695% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03020._colored.png

## 103/345: Finished rna_polymerase id: hsa03020 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03022._colored.png

## 104/345: Finished basal_transcription_factors id: hsa03022 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03030._colored.png

## 105/345: Finished dna_replication id: hsa03030 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03040._colored.png

## 106/345: Finished spliceosome id: hsa03040 with 3.333% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03050._colored.png

## 107/345: Finished proteasome id: hsa03050 with 18% genes mapped(5 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03060._colored.png

## 108/345: Finished protein_export id: hsa03060 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03320._colored.png

## 109/345: Finished ppar_signaling_pathway id: hsa03320 with 41.18% genes mapped(19 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03410._colored.png

## 110/345: Finished base_excision_repair id: hsa03410 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03420._colored.png

## 111/345: Finished nucleotide_excision_repair id: hsa03420 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03430._colored.png

## 112/345: Finished mismatch_repair id: hsa03430 with 5.263% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03440._colored.png

## 113/345: Finished homologous_recombination id: hsa03440 with 4.878% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03450._colored.png

## Info: some node width is different from others, and hence adjusted!

## 114/345: Finished non-homologous_end-joining id: hsa03450 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03460._colored.png

## Info: some node width is different from others, and hence adjusted!

## 115/345: Finished fanconi_anemia_pathway id: hsa03460 with 6.122% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04010._colored.png

## 116/345: Finished mapk_signaling_pathway id: hsa04010 with 13.45% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04012._colored.png

## 117/345: Finished erbb_signaling_pathway id: hsa04012 with 21.67% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04014._colored.png

## 118/345: Finished ras_signaling_pathway id: hsa04014 with 10.47% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04015._colored.png

## 119/345: Finished rap1_signaling_pathway id: hsa04015 with 13.75% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04020._colored.png

## 120/345: Finished calcium_signaling_pathway id: hsa04020 with 46.15% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04022._colored.png

## 121/345: Finished cgmp-pkg_signaling_pathway id: hsa04022 with 18.46% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04024._colored.png

## 122/345: Finished camp_signaling_pathway id: hsa04024 with 26.74% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04060._colored.png

## 123/345: Finished cytokine-cytokine_receptor_interaction id: hsa04060 with 29.3% genes mapped(86 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04061._colored.png

## 124/345: Finished viral_protein_interaction_with_cytokine_and_cytokine_receptor id: hsa04061 with 46.26% genes mapped(33 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04062._colored.png

## 125/345: Finished chemokine_signaling_pathway id: hsa04062 with 18.97% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04064._colored.png

## 126/345: Finished nf-kappa_b_signaling_pathway id: hsa04064 with 25.55% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04066._colored.png

## 127/345: Finished hif-1_signaling_pathway id: hsa04066 with 13.85% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04068._colored.png

## 128/345: Finished foxo_signaling_pathway id: hsa04068 with 17.5% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04070._colored.png

## 129/345: Finished phosphatidylinositol_signaling_system id: hsa04070 with 14.29% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04071._colored.png

## 130/345: Finished sphingolipid_signaling_pathway id: hsa04071 with 23.81% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04072._colored.png

## 131/345: Finished phospholipase_d_signaling_pathway id: hsa04072 with 26.79% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04080._colored.png

## 132/345: Finished neuroactive_ligand-receptor_interaction id: hsa04080 with 23.53% genes mapped(32 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04110._colored.png

## 133/345: Finished cell_cycle id: hsa04110 with 17.39% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04114._colored.png

## 134/345: Finished oocyte_meiosis id: hsa04114 with 26.76% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04115._colored.png

## 135/345: Finished p53_signaling_pathway id: hsa04115 with 12.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04120._colored.png

## 136/345: Finished ubiquitin_mediated_proteolysis id: hsa04120 with 6.25% genes mapped(7 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04122._colored.png

## 137/345: Finished sulfur_relay_system id: hsa04122 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04130._colored.png

## 138/345: Finished snare_interactions_in_vesicular_transport id: hsa04130 with 6.061% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04136._colored.png

## Info: some node width is different from others, and hence adjusted!

## 139/345: Finished autophagy_-_other id: hsa04136 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04137._colored.png

## 140/345: Finished mitophagy_-_animal id: hsa04137 with 6.122% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04140._colored.png

## 141/345: Finished autophagy_-_animal id: hsa04140 with 4.808% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04141._colored.png

## 142/345: Finished protein_processing_in_endoplasmic_reticulum id: hsa04141 with 6.061% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04142._colored.png

## Info: some node width is different from others, and hence adjusted!

## 143/345: Finished lysosome id: hsa04142 with 15.49% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04144._colored.png

## Info: some node width is different from others, and hence adjusted!

## 144/345: Finished endocytosis id: hsa04144 with 9.167% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04145._colored.png

## 145/345: Finished phagosome id: hsa04145 with 33.78% genes mapped(19 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04146._colored.png

## 146/345: Finished peroxisome id: hsa04146 with 7.692% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04150._colored.png

## 147/345: Finished mtor_signaling_pathway id: hsa04150 with 9.211% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04151._colored.png

## 148/345: Finished pi3k-akt_signaling_pathway id: hsa04151 with 16.67% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04152._colored.png

## 149/345: Finished ampk_signaling_pathway id: hsa04152 with 29.41% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04210._colored.png

## 150/345: Finished apoptosis id: hsa04210 with 16.04% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04211._colored.png

## 151/345: Finished longevity_regulating_pathway id: hsa04211 with 17.78% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04213._colored.png

## Info: some node width is different from others, and hence adjusted!

## 152/345: Finished longevity_regulating_pathway_-_multiple_species id: hsa04213 with 4.082% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04215._colored.png

## Info: some node width is different from others, and hence adjusted!

## 153/345: Finished apoptosis_-_multiple_species id: hsa04215 with 11.11% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04216._colored.png

## 154/345: Finished ferroptosis id: hsa04216 with 26.47% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04217._colored.png

## 155/345: Finished necroptosis id: hsa04217 with 17.11% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04218._colored.png

## 156/345: Finished cellular_senescence id: hsa04218 with 17.53% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04260._colored.png

## 157/345: Finished cardiac_muscle_contraction id: hsa04260 with 40.74% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04261._colored.png

## 158/345: Finished adrenergic_signaling_in_cardiomyocytes id: hsa04261 with 33.33% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04270._colored.png

## 159/345: Finished vascular_smooth_muscle_contraction id: hsa04270 with 20.75% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04310._colored.png

## 160/345: Finished wnt_signaling_pathway id: hsa04310 with 21.69% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04330._colored.png

## 161/345: Finished notch_signaling_pathway id: hsa04330 with 4% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04340._colored.png

## 162/345: Finished hedgehog_signaling_pathway id: hsa04340 with 30.51% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04350._colored.png

## 163/345: Finished tgf-beta_signaling_pathway id: hsa04350 with 13.89% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04360._colored.png

## 164/345: Finished axon_guidance id: hsa04360 with 17.27% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04370._colored.png

## 165/345: Finished vegf_signaling_pathway id: hsa04370 with 17.86% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04371._colored.png

## 166/345: Finished apelin_signaling_pathway id: hsa04371 with 22.58% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04380._colored.png

## 167/345: Finished osteoclast_differentiation id: hsa04380 with 21.13% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04390._colored.png

## 168/345: Finished hippo_signaling_pathway id: hsa04390 with 12.09% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04392._colored.png

## 169/345: Finished hippo_signaling_pathway_-_multiple_species id: hsa04392 with 10% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04510._colored.png

## 170/345: Finished focal_adhesion id: hsa04510 with 13.33% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04512._colored.png

## 171/345: Finished ecm-receptor_interaction id: hsa04512 with 32.23% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04514._colored.png

## 172/345: Finished cell_adhesion_molecules id: hsa04514 with 28.63% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04520._colored.png

## 173/345: Finished adherens_junction id: hsa04520 with 12.16% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04530._colored.png

## 174/345: Finished tight_junction id: hsa04530 with 24.62% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04540._colored.png

## 175/345: Finished gap_junction id: hsa04540 with 33.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04550._colored.png

## 176/345: Finished signaling_pathways_regulating_pluripotency_of_stem_cells id: hsa04550 with 18.37% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04610._colored.png

## 177/345: Finished complement_and_coagulation_cascades id: hsa04610 with 23.53% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04611._colored.png

## Info: some node width is different from others, and hence adjusted!

## 178/345: Finished platelet_activation id: hsa04611 with 17.39% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04612._colored.png

## 179/345: Finished antigen_processing_and_presentation id: hsa04612 with 43.59% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04613._colored.png

## 180/345: Finished neutrophil_extracellular_trap_formation id: hsa04613 with 25.88% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04614._colored.png

## 181/345: Finished renin-angiotensin_system id: hsa04614 with 34.48% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04620._colored.png

## 182/345: Finished toll-like_receptor_signaling_pathway id: hsa04620 with 22.78% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04621._colored.png

## Info: some node width is different from others, and hence adjusted!

## 183/345: Finished nod-like_receptor_signaling_pathway id: hsa04621 with 23.03% genes mapped(29 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04622._colored.png

## 184/345: Finished rig-i-like_receptor_signaling_pathway id: hsa04622 with 15.38% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04623._colored.png

## 185/345: Finished cytosolic_dna-sensing_pathway id: hsa04623 with 25.81% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04625._colored.png

## 186/345: Finished c-type_lectin_receptor_signaling_pathway id: hsa04625 with 32.47% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04630._colored.png

## 187/345: Finished jak-stat_signaling_pathway id: hsa04630 with 22.86% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04640._colored.png

## 188/345: Finished hematopoietic_cell_lineage id: hsa04640 with 44.53% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04650._colored.png

## 189/345: Finished natural_killer_cell_mediated_cytotoxicity id: hsa04650 with 36.26% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04657._colored.png

## 190/345: Finished il-17_signaling_pathway id: hsa04657 with 29.67% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04658._colored.png

## Info: some node width is different from others, and hence adjusted!

## 191/345: Finished th1_and_th2_cell_differentiation id: hsa04658 with 21.54% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04659._colored.png

## 192/345: Finished th17_cell_differentiation id: hsa04659 with 23.08% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04660._colored.png

## Info: some node width is different from others, and hence adjusted!

## 193/345: Finished t_cell_receptor_signaling_pathway id: hsa04660 with 12.12% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04662._colored.png

## 194/345: Finished b_cell_receptor_signaling_pathway id: hsa04662 with 8.889% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04664._colored.png

## 195/345: Finished fc_epsilon_ri_signaling_pathway id: hsa04664 with 26.19% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04666._colored.png

## 196/345: Finished fc_gamma_r-mediated_phagocytosis id: hsa04666 with 17.02% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04668._colored.png

## 197/345: Finished tnf_signaling_pathway id: hsa04668 with 28.57% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04670._colored.png

## 198/345: Finished leukocyte_transendothelial_migration id: hsa04670 with 10.13% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04672._colored.png

## 199/345: Finished intestinal_immune_network_for_iga_production id: hsa04672 with 27.78% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04710._colored.png

## 200/345: Finished circadian_rhythm id: hsa04710 with 5.882% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04713._colored.png

## 201/345: Finished circadian_entrainment id: hsa04713 with 45.65% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04714._colored.png

## 202/345: Finished thermogenesis id: hsa04714 with 14.81% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04720._colored.png

## 203/345: Finished long-term_potentiation id: hsa04720 with 16% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04721._colored.png

## 204/345: Finished synaptic_vesicle_cycle id: hsa04721 with 27.59% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04722._colored.png

## 205/345: Finished neurotrophin_signaling_pathway id: hsa04722 with 15.58% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04723._colored.png

## Info: some node width is different from others, and hence adjusted!
## Info: some node width is different from others, and hence adjusted!

## 206/345: Finished retrograde_endocannabinoid_signaling id: hsa04723 with 39.02% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04724._colored.png

## 207/345: Finished glutamatergic_synapse id: hsa04724 with 35.42% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04725._colored.png

## 208/345: Finished cholinergic_synapse id: hsa04725 with 17.5% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04726._colored.png

## 209/345: Finished serotonergic_synapse id: hsa04726 with 29.79% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04727._colored.png

## 210/345: Finished gabaergic_synapse id: hsa04727 with 35.14% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04728._colored.png

## 211/345: Finished dopaminergic_synapse id: hsa04728 with 25% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04730._colored.png

## 212/345: Finished long-term_depression id: hsa04730 with 33.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04740._colored.png

## Info: some node width is different from others, and hence adjusted!

## 213/345: Finished olfactory_transduction id: hsa04740 with 36% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04742._colored.png

## Info: some node width is different from others, and hence adjusted!

## 214/345: Finished taste_transduction id: hsa04742 with 14.71% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04744._colored.png

## 215/345: Finished phototransduction id: hsa04744 with 7.143% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04750._colored.png

## 216/345: Finished inflammatory_mediator_regulation_of_trp_channels id: hsa04750 with 22.45% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04810._colored.png

## 217/345: Finished regulation_of_actin_cytoskeleton id: hsa04810 with 9.211% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04910._colored.png

## 218/345: Finished insulin_signaling_pathway id: hsa04910 with 20.97% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04911._colored.png

## 219/345: Finished insulin_secretion id: hsa04911 with 25.64% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04912._colored.png

## 220/345: Finished gnrh_signaling_pathway id: hsa04912 with 12.2% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04913._colored.png

## 221/345: Finished ovarian_steroidogenesis id: hsa04913 with 26.67% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04914._colored.png

## 222/345: Finished progesterone-mediated_oocyte_maturation id: hsa04914 with 31.58% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04915._colored.png

## 223/345: Finished estrogen_signaling_pathway id: hsa04915 with 22.58% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04916._colored.png

## 224/345: Finished melanogenesis id: hsa04916 with 39.47% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04917._colored.png

## 225/345: Finished prolactin_signaling_pathway id: hsa04917 with 11.11% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04918._colored.png

## 226/345: Finished thyroid_hormone_synthesis id: hsa04918 with 16.67% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04919._colored.png

## 227/345: Finished thyroid_hormone_signaling_pathway id: hsa04919 with 15.38% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04920._colored.png

## 228/345: Finished adipocytokine_signaling_pathway id: hsa04920 with 38.89% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04921._colored.png

## 229/345: Finished oxytocin_signaling_pathway id: hsa04921 with 25.86% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04922._colored.png

## 230/345: Finished glucagon_signaling_pathway id: hsa04922 with 30% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04923._colored.png

## 231/345: Finished regulation_of_lipolysis_in_adipocytes id: hsa04923 with 33.33% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04924._colored.png

## 232/345: Finished renin_secretion id: hsa04924 with 40% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04925._colored.png

## 233/345: Finished aldosterone_synthesis_and_secretion id: hsa04925 with 26.83% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04926._colored.png

## 234/345: Finished relaxin_signaling_pathway id: hsa04926 with 28.4% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04927._colored.png

## 235/345: Finished cortisol_synthesis_and_secretion id: hsa04927 with 24.39% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04928._colored.png

## 236/345: Finished parathyroid_hormone_synthesis,_secretion_and_action id: hsa04928 with 21.21% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04929._colored.png

## 237/345: Finished gnrh_secretion id: hsa04929 with 12.12% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04930._colored.png

## 238/345: Finished type_ii_diabetes_mellitus id: hsa04930 with 36% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04931._colored.png

## 239/345: Finished insulin_resistance id: hsa04931 with 29.29% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04932._colored.png

## 240/345: Finished non-alcoholic_fatty_liver_disease id: hsa04932 with 26.47% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04933._colored.png

## 241/345: Finished age-rage_signaling_pathway_in_diabetic_complications id: hsa04933 with 25.81% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04934._colored.png

## 242/345: Finished cushing_syndrome id: hsa04934 with 21.84% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04935._colored.png

## 243/345: Finished growth_hormone_synthesis,_secretion_and_action id: hsa04935 with 20% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04936._colored.png

## 244/345: Finished alcoholic_liver_disease id: hsa04936 with 23.85% genes mapped(19 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04940._colored.png

## 245/345: Finished type_i_diabetes_mellitus id: hsa04940 with 57.14% genes mapped(11 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04950._colored.png

## 246/345: Finished maturity_onset_diabetes_of_the_young id: hsa04950 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04960._colored.png

## 247/345: Finished aldosterone-regulated_sodium_reabsorption id: hsa04960 with 21.05% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04961._colored.png

## 248/345: Finished endocrine_and_other_factor-regulated_calcium_reabsorption id: hsa04961 with 22.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04962._colored.png

## 249/345: Finished vasopressin-regulated_water_reabsorption id: hsa04962 with 4.348% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04964._colored.png

## 250/345: Finished proximal_tubule_bicarbonate_reclamation id: hsa04964 with 23.08% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04966._colored.png

## 251/345: Finished collecting_duct_acid_secretion id: hsa04966 with 16.67% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04970._colored.png

## 252/345: Finished salivary_secretion id: hsa04970 with 35% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04971._colored.png

## 253/345: Finished gastric_acid_secretion id: hsa04971 with 36.67% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04972._colored.png

## 254/345: Finished pancreatic_secretion id: hsa04972 with 29.79% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04973._colored.png

## 255/345: Finished carbohydrate_digestion_and_absorption id: hsa04973 with 27.27% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04974._colored.png

## Info: some node width is different from others, and hence adjusted!

## 256/345: Finished protein_digestion_and_absorption id: hsa04974 with 37.04% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04975._colored.png

## 257/345: Finished fat_digestion_and_absorption id: hsa04975 with 15.62% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04976._colored.png

## 258/345: Finished bile_secretion id: hsa04976 with 15.62% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04977._colored.png

## 259/345: Finished vitamin_digestion_and_absorption id: hsa04977 with 2.632% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04978._colored.png

## 260/345: Finished mineral_absorption id: hsa04978 with 32.35% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04979._colored.png

## 261/345: Finished cholesterol_metabolism id: hsa04979 with 16.25% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05010._colored.png

## 262/345: Finished alzheimer_disease id: hsa05010 with 17.29% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05012._colored.png

## 263/345: Finished parkinson_disease id: hsa05012 with 11.65% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05014._colored.png

## 264/345: Finished amyotrophic_lateral_sclerosis id: hsa05014 with 4.286% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05016._colored.png

## 265/345: Finished huntington_disease id: hsa05016 with 10.89% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05017._colored.png

## 266/345: Finished spinocerebellar_ataxia id: hsa05017 with 11.9% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05020._colored.png

## 267/345: Finished prion_disease id: hsa05020 with 13.46% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05022._colored.png

## 268/345: Finished pathways_of_neurodegeneration_-_multiple_diseases id: hsa05022 with 12.4% genes mapped(25 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05030._colored.png

## 269/345: Finished cocaine_addiction id: hsa05030 with 30.61% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05031._colored.png

## 270/345: Finished amphetamine_addiction id: hsa05031 with 32.79% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05032._colored.png

## 271/345: Finished morphine_addiction id: hsa05032 with 27.27% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05033._colored.png

## 272/345: Finished nicotine_addiction id: hsa05033 with 30.77% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05034._colored.png

## 273/345: Finished alcoholism id: hsa05034 with 25.81% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05100._colored.png

## Info: some node width is different from others, and hence adjusted!

## 274/345: Finished bacterial_invasion_of_epithelial_cells id: hsa05100 with 6.818% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05110._colored.png

## 275/345: Finished vibrio_cholerae_infection id: hsa05110 with 17.65% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05120._colored.png

## 276/345: Finished epithelial_cell_signaling_in_helicobacter_pylori_infection id: hsa05120 with 29.41% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05130._colored.png

## 277/345: Finished pathogenic_escherichia_coli_infection id: hsa05130 with 12.17% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05131._colored.png

## 278/345: Finished shigellosis id: hsa05131 with 12.1% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05132._colored.png

## Info: some node width is different from others, and hence adjusted!

## 279/345: Finished salmonella_infection id: hsa05132 with 12.08% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05133._colored.png

## 280/345: Finished pertussis id: hsa05133 with 29.63% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05134._colored.png

## Info: some node width is different from others, and hence adjusted!

## 281/345: Finished legionellosis id: hsa05134 with 28.89% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05135._colored.png

## 282/345: Finished yersinia_infection id: hsa05135 with 11.96% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05140._colored.png

## 283/345: Finished leishmaniasis id: hsa05140 with 30.43% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05142._colored.png

## 284/345: Finished chagas_disease id: hsa05142 with 34.85% genes mapped(18 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05143._colored.png

## 285/345: Finished african_trypanosomiasis id: hsa05143 with 37.93% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05144._colored.png

## 286/345: Finished malaria id: hsa05144 with 43.59% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05145._colored.png

## 287/345: Finished toxoplasmosis id: hsa05145 with 29.31% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05146._colored.png

## 288/345: Finished amoebiasis id: hsa05146 with 47.83% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05150._colored.png

## 289/345: Finished staphylococcus_aureus_infection id: hsa05150 with 39.47% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05152._colored.png

## 290/345: Finished tuberculosis id: hsa05152 with 24.53% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05160._colored.png

## 291/345: Finished hepatitis_c id: hsa05160 with 19.78% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05161._colored.png

## Info: some node width is different from others, and hence adjusted!

## 292/345: Finished hepatitis_b id: hsa05161 with 17.83% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05162._colored.png

## 293/345: Finished measles id: hsa05162 with 22.09% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05163._colored.png

## Info: some node width is different from others, and hence adjusted!

## 294/345: Finished human_cytomegalovirus_infection id: hsa05163 with 24.83% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05164._colored.png

## 295/345: Finished influenza_a id: hsa05164 with 21.82% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05165._colored.png

## 296/345: Finished human_papillomavirus_infection id: hsa05165 with 17.61% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05166._colored.png

## Info: some node width is different from others, and hence adjusted!

## 297/345: Finished human_t-cell_leukemia_virus_1_infection id: hsa05166 with 21.67% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05167._colored.png

## Info: some node width is different from others, and hence adjusted!

## 298/345: Finished kaposi_sarcoma-associated_herpesvirus_infection id: hsa05167 with 23.39% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05168._colored.png

## 299/345: Finished herpes_simplex_virus_1_infection id: hsa05168 with 25.2% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05169._colored.png

## 300/345: Finished epstein-barr_virus_infection id: hsa05169 with 18.94% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05170._colored.png

## 301/345: Finished human_immunodeficiency_virus_1_infection id: hsa05170 with 19.01% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05171._colored.png

## 302/345: Finished coronavirus_disease_-_covid-19 id: hsa05171 with 40% genes mapped(29 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05200._colored.png

## Info: some node width is different from others, and hence adjusted!

## 303/345: Finished pathways_in_cancer id: hsa05200 with 22.94% genes mapped(53 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05202._colored.png

## 304/345: Finished transcriptional_misregulation_in_cancer id: hsa05202 with 17.79% genes mapped(28 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05203._colored.png

## 305/345: Finished viral_carcinogenesis id: hsa05203 with 15.22% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05204._colored.png

## 306/345: Finished chemical_carcinogenesis_-_dna_adducts id: hsa05204 with 23.68% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05205._colored.png

## 307/345: Finished proteoglycans_in_cancer id: hsa05205 with 11.67% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05206._colored.png

## Info: some node width is different from others, and hence adjusted!

## 308/345: Finished micrornas_in_cancer id: hsa05206 with 4.889% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05207._colored.png

## 309/345: Finished chemical_carcinogenesis_-_receptor_activation id: hsa05207 with 19.05% genes mapped(18 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05208._colored.png

## 310/345: Finished chemical_carcinogenesis_-_reactive_oxygen_species id: hsa05208 with 16.25% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05210._colored.png

## 311/345: Finished colorectal_cancer id: hsa05210 with 9.722% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05211._colored.png

## 312/345: Finished renal_cell_carcinoma id: hsa05211 with 9.259% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05212._colored.png

## 313/345: Finished pancreatic_cancer id: hsa05212 with 13.46% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05213._colored.png

## 314/345: Finished endometrial_cancer id: hsa05213 with 8.889% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05214._colored.png

## Info: some node width is different from others, and hence adjusted!

## 315/345: Finished glioma id: hsa05214 with 14.06% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05215._colored.png

## 316/345: Finished prostate_cancer id: hsa05215 with 20% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05216._colored.png

## 317/345: Finished thyroid_cancer id: hsa05216 with 15.38% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05217._colored.png

## 318/345: Finished basal_cell_carcinoma id: hsa05217 with 36% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05218._colored.png

## 319/345: Finished melanoma id: hsa05218 with 9.375% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05219._colored.png

## Info: some node width is different from others, and hence adjusted!

## 320/345: Finished bladder_cancer id: hsa05219 with 21.88% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05220._colored.png

## 321/345: Finished chronic_myeloid_leukemia id: hsa05220 with 7.843% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05221._colored.png

## 322/345: Finished acute_myeloid_leukemia id: hsa05221 with 22.92% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05222._colored.png

## 323/345: Finished small_cell_lung_cancer id: hsa05222 with 13.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05223._colored.png

## 324/345: Finished non-small_cell_lung_cancer id: hsa05223 with 9.804% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05224._colored.png

## 325/345: Finished breast_cancer id: hsa05224 with 18.27% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05225._colored.png

## 326/345: Finished hepatocellular_carcinoma id: hsa05225 with 11.58% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05226._colored.png

## 327/345: Finished gastric_cancer id: hsa05226 with 14.44% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05230._colored.png

## 328/345: Finished central_carbon_metabolism_in_cancer id: hsa05230 with 18.64% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05231._colored.png

## 329/345: Finished choline_metabolism_in_cancer id: hsa05231 with 12.5% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05235._colored.png

## 330/345: Finished pd-l1_expression_and_pd-1_checkpoint_pathway_in_cancer id: hsa05235 with 12.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05310._colored.png

## 331/345: Finished asthma id: hsa05310 with 25% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05320._colored.png

## 332/345: Finished autoimmune_thyroid_disease id: hsa05320 with 44.74% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05321._colored.png

## 333/345: Finished inflammatory_bowel_disease id: hsa05321 with 36.51% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05322._colored.png

## 334/345: Finished systemic_lupus_erythematosus id: hsa05322 with 39.58% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05323._colored.png

## 335/345: Finished rheumatoid_arthritis id: hsa05323 with 53.06% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05330._colored.png

## 336/345: Finished allograft_rejection id: hsa05330 with 63.33% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05332._colored.png

## 337/345: Finished graft-versus-host_disease id: hsa05332 with 81.82% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05340._colored.png

## 338/345: Finished primary_immunodeficiency id: hsa05340 with 6.25% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05410._colored.png

## 339/345: Finished hypertrophic_cardiomyopathy id: hsa05410 with 30% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05412._colored.png

## 340/345: Finished arrhythmogenic_right_ventricular_cardiomyopathy id: hsa05412 with 20.34% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05414._colored.png

## 341/345: Finished dilated_cardiomyopathy id: hsa05414 with 30% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05415._colored.png

## 342/345: Finished diabetic_cardiomyopathy id: hsa05415 with 17.86% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05416._colored.png

## 343/345: Finished viral_myocarditis id: hsa05416 with 29.41% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05417._colored.png

## Info: some node width is different from others, and hence adjusted!

## 344/345: Finished lipid_and_atherosclerosis id: hsa05417 with 26.46% genes mapped(27 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05418._colored.png

## 345/345: Finished fluid_shear_stress_and_atherosclerosis id: hsa05418 with 16.13% genes mapped(13 unique).

                           ## id_column = "kegg_prefix_id")

5 Add compounds and genes

We have a csv/tsv file of pathways and compounds. It is in a peculiar format and does not have any information about the range of increase/decrease. As a result, I do not think we can meaningfully scale the data; but we can extract all the compound IDs and set their color.

compound_start <- readr::read_csv("downloaded_data/joint_metaboanalyst.csv")

## New names:
## * `` -> ...1

## Warning: One or more parsing issues, see `problems()` for details

## Rows: 68 Columns: 2

## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): ...1, matched_features;;;;;;;;;;;;;;;

## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

pile_of_compounds_and_junk <- compound_start[[2]]
split_stuff <- strsplit(x = pile_of_compounds_and_junk, split = "; ")
compounds <- c()
for (i in 1:length(split_stuff)) {
  internal <- split_stuff[[i]]
  cpd_idx <- grep("^cpd", internal)
  internal <- internal[cpd_idx]
  internal_ids <- stringi::stri_replace_all_fixed(internal, ";", "")
  internal_ids <- gsub(pattern = "^cpd:", replacement = "", x = internal_ids)
  compounds <- c(internal_ids, compounds)
}
compounds <- unique(compounds)
compound_input <- rep(10, length(compounds))
names(compound_input) <- compounds


testing <- simple_pathview(gene_input = pathview_input, compound_input = compound_input,
                           species = "hsa",
                           fc_column = "deseq_logfc",
                           id_column = "entrezgene_id")

## Here are some path gene examples: gn:T01001, 10327, 124, 125, 126, 127

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 9 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00010._colored.png

## 1/345: Finished glycolysis_/_gluconeogenesis id: hsa00010 with 22.86% genes mapped(7 unique).

## Here are some path gene examples: gn:T01001, 1431, 1737, 1738, 1743, 2271

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 1 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00020._colored.png

## 2/345: Finished citrate_cycle_(tca_cycle) id: hsa00020 with 4.545% genes mapped(1 unique).

## Here are some path gene examples: gn:T01001, 132158, 2203, 221823, 226, 229

## Here are your genes: 2268, 1080, 51056, 55365, 90293, 6542

## There were 2 overlapping genes observed.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00030._colored.png

## 3/345: Finished pentose_phosphate_pathway id: hsa00030 with 7.692% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00040._colored.png

## 4/345: Finished pentose_and_glucuronate_interconversions id: hsa00040 with 14.29% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00051._colored.png

## 5/345: Finished fructose_and_mannose_metabolism id: hsa00051 with 20% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00052._colored.png

## 6/345: Finished galactose_metabolism id: hsa00052 with 8.333% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00053._colored.png

## 7/345: Finished ascorbate_and_aldarate_metabolism id: hsa00053 with 37.5% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00061._colored.png

## 8/345: Finished fatty_acid_biosynthesis id: hsa00061 with 3.297% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00062._colored.png

## Info: some node width is different from others, and hence adjusted!

## 9/345: Finished fatty_acid_elongation id: hsa00062 with 5.128% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00071._colored.png

## 10/345: Finished fatty_acid_degradation id: hsa00071 with 6.349% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00100._colored.png

## 11/345: Finished steroid_biosynthesis id: hsa00100 with 45% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00120._colored.png

## 12/345: Finished primary_bile_acid_biosynthesis id: hsa00120 with 15.22% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00130._colored.png

## 13/345: Finished ubiquinone_and_other_terpenoid-quinone_biosynthesis id: hsa00130 with 14.29% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00140._colored.png

## 14/345: Finished steroid_hormone_biosynthesis id: hsa00140 with 25.47% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00190._colored.png

## Info: some node width is different from others, and hence adjusted!
## Info: some node width is different from others, and hence adjusted!

## 15/345: Finished oxidative_phosphorylation id: hsa00190 with 4.425% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00220._colored.png

## 16/345: Finished arginine_biosynthesis id: hsa00220 with 38.46% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00230._colored.png

## 17/345: Finished purine_metabolism id: hsa00230 with 15.53% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00232._colored.png

## 18/345: Finished caffeine_metabolism id: hsa00232 with 44.44% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00240._colored.png

## 19/345: Finished pyrimidine_metabolism id: hsa00240 with 21.21% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00250._colored.png

## 20/345: Finished alanine,_aspartate_and_glutamate_metabolism id: hsa00250 with 18.18% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00260._colored.png

## 21/345: Finished glycine,_serine_and_threonine_metabolism id: hsa00260 with 30.56% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00270._colored.png

## 22/345: Finished cysteine_and_methionine_metabolism id: hsa00270 with 13.16% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00280._colored.png

## 23/345: Finished valine,_leucine_and_isoleucine_degradation id: hsa00280 with 6% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00290._colored.png

## 24/345: Finished valine,_leucine_and_isoleucine_biosynthesis id: hsa00290 with 25% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00310._colored.png

## 25/345: Finished lysine_degradation id: hsa00310 with 20.83% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00330._colored.png

## 26/345: Finished arginine_and_proline_metabolism id: hsa00330 with 30.77% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00340._colored.png

## 27/345: Finished histidine_metabolism id: hsa00340 with 31.25% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00350._colored.png

## 28/345: Finished tyrosine_metabolism id: hsa00350 with 56.52% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00360._colored.png

## 29/345: Finished phenylalanine_metabolism id: hsa00360 with 40% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00380._colored.png

## 30/345: Finished tryptophan_metabolism id: hsa00380 with 41.86% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00400._colored.png

## 31/345: Finished phenylalanine,_tyrosine_and_tryptophan_biosynthesis id: hsa00400 with 28.57% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00410._colored.png

## 32/345: Finished beta-alanine_metabolism id: hsa00410 with 13.04% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00430._colored.png

## 33/345: Finished taurine_and_hypotaurine_metabolism id: hsa00430 with 25% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00440._colored.png

## 34/345: Finished phosphonate_and_phosphinate_metabolism id: hsa00440 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00450._colored.png

## 35/345: Finished selenocompound_metabolism id: hsa00450 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00470._colored.png

## 36/345: Finished d-amino_acid_metabolism id: hsa00470 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00480._colored.png

## 37/345: Finished glutathione_metabolism id: hsa00480 with 41.38% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00500._colored.png

## Info: some node width is different from others, and hence adjusted!

## 38/345: Finished starch_and_sucrose_metabolism id: hsa00500 with 16% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00510._colored.png

## 39/345: Finished n-glycan_biosynthesis id: hsa00510 with 5.128% genes mapped(2 unique).

## Warning: Number of mappable nodes is below 3, hsa00511 skipped!

## Warning in simple_pathview(gene_input = pathview_input, compound_input =
## compound_input, : There was a failure for: hsa00511.

## 40/345: Finished other_glycan_degradation id: hsa00511 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00512._colored.png

## 41/345: Finished mucin_type_o-glycan_biosynthesis id: hsa00512 with 7.692% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00513._colored.png

## 42/345: Finished various_types_of_n-glycan_biosynthesis id: hsa00513 with 3.333% genes mapped(1 unique).

## Warning: Number of mappable nodes is below 3, hsa00514 skipped!

## Warning in simple_pathview(gene_input = pathview_input, compound_input =
## compound_input, : There was a failure for: hsa00514.

## 43/345: Finished other_types_of_o-glycan_biosynthesis id: hsa00514 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00515._colored.png

## 44/345: Finished mannose_type_o-glycan_biosynthesis id: hsa00515 with 13.64% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00520._colored.png

## 45/345: Finished amino_sugar_and_nucleotide_sugar_metabolism id: hsa00520 with 18.37% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00524._colored.png

## 46/345: Finished neomycin,_kanamycin_and_gentamicin_biosynthesis id: hsa00524 with 50% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00531._colored.png

## 47/345: Finished glycosaminoglycan_degradation id: hsa00531 with 19.05% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00532._colored.png

## 48/345: Finished glycosaminoglycan_biosynthesis_-_chondroitin_sulfate_/_dermatan_sulfate id: hsa00532 with 5.263% genes mapped(1 unique).

## Warning: Number of mappable nodes is below 3, hsa00533 skipped!

## Warning in simple_pathview(gene_input = pathview_input, compound_input =
## compound_input, : There was a failure for: hsa00533.

## 49/345: Finished glycosaminoglycan_biosynthesis_-_keratan_sulfate id: hsa00533 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00534._colored.png

## 50/345: Finished glycosaminoglycan_biosynthesis_-_heparan_sulfate_/_heparin id: hsa00534 with 13.04% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00561._colored.png

## 51/345: Finished glycerolipid_metabolism id: hsa00561 with 52.63% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00562._colored.png

## 52/345: Finished inositol_phosphate_metabolism id: hsa00562 with 7.692% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00563._colored.png

## 53/345: Finished glycosylphosphatidylinositol_(gpi)-anchor_biosynthesis id: hsa00563 with 3.846% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00564._colored.png

## 54/345: Finished glycerophospholipid_metabolism id: hsa00564 with 21.57% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00565._colored.png

## 55/345: Finished ether_lipid_metabolism id: hsa00565 with 15% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00590._colored.png

## 56/345: Finished arachidonic_acid_metabolism id: hsa00590 with 57.14% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00591._colored.png

## 57/345: Finished linoleic_acid_metabolism id: hsa00591 with 33.33% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00592._colored.png

## 58/345: Finished alpha-linolenic_acid_metabolism id: hsa00592 with 11.11% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00600._colored.png

## 59/345: Finished sphingolipid_metabolism id: hsa00600 with 36.11% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00601._colored.png

## 60/345: Finished glycosphingolipid_biosynthesis_-_lacto_and_neolacto_series id: hsa00601 with 5.333% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00603._colored.png

## 61/345: Finished glycosphingolipid_biosynthesis_-_globo_and_isoglobo_series id: hsa00603 with 5.882% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00604._colored.png

## 62/345: Finished glycosphingolipid_biosynthesis_-_ganglio_series id: hsa00604 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00620._colored.png

## 63/345: Finished pyruvate_metabolism id: hsa00620 with 20% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00630._colored.png

## 64/345: Finished glyoxylate_and_dicarboxylate_metabolism id: hsa00630 with 8.333% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00640._colored.png

## 65/345: Finished propanoate_metabolism id: hsa00640 with 4.167% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00650._colored.png

## 66/345: Finished butanoate_metabolism id: hsa00650 with 21.43% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00670._colored.png

## 67/345: Finished one_carbon_pool_by_folate id: hsa00670 with 4.545% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00730._colored.png

## 68/345: Finished thiamine_metabolism id: hsa00730 with 28.57% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00740._colored.png

## 69/345: Finished riboflavin_metabolism id: hsa00740 with 40% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00750._colored.png

## 70/345: Finished vitamin_b6_metabolism id: hsa00750 with 8.333% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00760._colored.png

## 71/345: Finished nicotinate_and_nicotinamide_metabolism id: hsa00760 with 37.04% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00770._colored.png

## 72/345: Finished pantothenate_and_coa_biosynthesis id: hsa00770 with 31.25% genes mapped(3 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00780._colored.png

## 73/345: Finished biotin_metabolism id: hsa00780 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00785._colored.png

## 74/345: Finished lipoic_acid_metabolism id: hsa00785 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00790._colored.png

## 75/345: Finished folate_biosynthesis id: hsa00790 with 20.59% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00830._colored.png

## 76/345: Finished retinol_metabolism id: hsa00830 with 35.14% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00860._colored.png

## 77/345: Finished porphyrin_metabolism id: hsa00860 with 4.167% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00900._colored.png

## 78/345: Finished terpenoid_backbone_biosynthesis id: hsa00900 with 11.11% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00910._colored.png

## 79/345: Finished nitrogen_metabolism id: hsa00910 with 75% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00920._colored.png

## 80/345: Finished sulfur_metabolism id: hsa00920 with 30% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00970._colored.png

## 81/345: Finished aminoacyl-trna_biosynthesis id: hsa00970 with 6.522% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00980._colored.png

## 82/345: Finished metabolism_of_xenobiotics_by_cytochrome_p450 id: hsa00980 with 27.91% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00982._colored.png

## 83/345: Finished drug_metabolism_-_cytochrome_p450 id: hsa00982 with 18.03% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa00983._colored.png

## 84/345: Finished drug_metabolism_-_other_enzymes id: hsa00983 with 19.51% genes mapped(7 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01040._colored.png

## 85/345: Finished biosynthesis_of_unsaturated_fatty_acids id: hsa01040 with 0% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01100._colored.png

## 86/345: Finished metabolic_pathways id: hsa01100 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01200._colored.png

## Info: some node width is different from others, and hence adjusted!

## 87/345: Finished carbon_metabolism id: hsa01200 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01210._colored.png

## 88/345: Finished 2-oxocarboxylic_acid_metabolism id: hsa01210 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01212._colored.png

## Info: some node width is different from others, and hence adjusted!

## 89/345: Finished fatty_acid_metabolism id: hsa01212 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01230._colored.png

## 90/345: Finished biosynthesis_of_amino_acids id: hsa01230 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01240._colored.png

## 91/345: Finished biosynthesis_of_cofactors id: hsa01240 with NaN% genes mapped(0 unique).

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01250._colored.png

## 92/345: Finished biosynthesis_of_nucleotide_sugars id: hsa01250 with NaN% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01521._colored.png

## 93/345: Finished egfr_tyrosine_kinase_inhibitor_resistance id: hsa01521 with 20.34% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01522._colored.png

## 94/345: Finished endocrine_resistance id: hsa01522 with 10% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01523._colored.png

## 95/345: Finished antifolate_resistance id: hsa01523 with 19.23% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa01524._colored.png

## 96/345: Finished platinum_drug_resistance id: hsa01524 with 8.511% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa02010._colored.png

## 97/345: Finished abc_transporters id: hsa02010 with 24.44% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03008._colored.png

## 98/345: Finished ribosome_biogenesis_in_eukaryotes id: hsa03008 with 1.613% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03010._colored.png

## 99/345: Finished ribosome id: hsa03010 with 0.8065% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03013._colored.png

## 100/345: Finished nucleocytoplasmic_transport id: hsa03013 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03015._colored.png

## 101/345: Finished mrna_surveillance_pathway id: hsa03015 with 3.509% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03018._colored.png

## 102/345: Finished rna_degradation id: hsa03018 with 1.695% genes mapped(1 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03020._colored.png

## 103/345: Finished rna_polymerase id: hsa03020 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03022._colored.png

## 104/345: Finished basal_transcription_factors id: hsa03022 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03030._colored.png

## 105/345: Finished dna_replication id: hsa03030 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03040._colored.png

## 106/345: Finished spliceosome id: hsa03040 with 3.333% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03050._colored.png

## 107/345: Finished proteasome id: hsa03050 with 18% genes mapped(5 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03060._colored.png

## 108/345: Finished protein_export id: hsa03060 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03320._colored.png

## 109/345: Finished ppar_signaling_pathway id: hsa03320 with 41.18% genes mapped(19 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03410._colored.png

## 110/345: Finished base_excision_repair id: hsa03410 with 0% genes mapped(0 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03420._colored.png

## 111/345: Finished nucleotide_excision_repair id: hsa03420 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03430._colored.png

## 112/345: Finished mismatch_repair id: hsa03430 with 5.263% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03440._colored.png

## 113/345: Finished homologous_recombination id: hsa03440 with 4.878% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03450._colored.png

## Info: some node width is different from others, and hence adjusted!

## 114/345: Finished non-homologous_end-joining id: hsa03450 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa03460._colored.png

## Info: some node width is different from others, and hence adjusted!

## 115/345: Finished fanconi_anemia_pathway id: hsa03460 with 6.122% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04010._colored.png

## 116/345: Finished mapk_signaling_pathway id: hsa04010 with 13.45% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04012._colored.png

## 117/345: Finished erbb_signaling_pathway id: hsa04012 with 21.67% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04014._colored.png

## 118/345: Finished ras_signaling_pathway id: hsa04014 with 10.47% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04015._colored.png

## 119/345: Finished rap1_signaling_pathway id: hsa04015 with 13.75% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04020._colored.png

## 120/345: Finished calcium_signaling_pathway id: hsa04020 with 46.15% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04022._colored.png

## 121/345: Finished cgmp-pkg_signaling_pathway id: hsa04022 with 18.46% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04024._colored.png

## 122/345: Finished camp_signaling_pathway id: hsa04024 with 26.74% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04060._colored.png

## 123/345: Finished cytokine-cytokine_receptor_interaction id: hsa04060 with 29.3% genes mapped(86 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04061._colored.png

## 124/345: Finished viral_protein_interaction_with_cytokine_and_cytokine_receptor id: hsa04061 with 46.26% genes mapped(33 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04062._colored.png

## 125/345: Finished chemokine_signaling_pathway id: hsa04062 with 18.97% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04064._colored.png

## 126/345: Finished nf-kappa_b_signaling_pathway id: hsa04064 with 25.55% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04066._colored.png

## 127/345: Finished hif-1_signaling_pathway id: hsa04066 with 13.85% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04068._colored.png

## 128/345: Finished foxo_signaling_pathway id: hsa04068 with 17.5% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04070._colored.png

## 129/345: Finished phosphatidylinositol_signaling_system id: hsa04070 with 14.29% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04071._colored.png

## 130/345: Finished sphingolipid_signaling_pathway id: hsa04071 with 23.81% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04072._colored.png

## 131/345: Finished phospholipase_d_signaling_pathway id: hsa04072 with 26.79% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04080._colored.png

## 132/345: Finished neuroactive_ligand-receptor_interaction id: hsa04080 with 23.53% genes mapped(32 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04110._colored.png

## 133/345: Finished cell_cycle id: hsa04110 with 17.39% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04114._colored.png

## 134/345: Finished oocyte_meiosis id: hsa04114 with 26.76% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04115._colored.png

## 135/345: Finished p53_signaling_pathway id: hsa04115 with 12.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04120._colored.png

## 136/345: Finished ubiquitin_mediated_proteolysis id: hsa04120 with 6.25% genes mapped(7 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04122._colored.png

## 137/345: Finished sulfur_relay_system id: hsa04122 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04130._colored.png

## 138/345: Finished snare_interactions_in_vesicular_transport id: hsa04130 with 6.061% genes mapped(2 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04136._colored.png

## Info: some node width is different from others, and hence adjusted!

## 139/345: Finished autophagy_-_other id: hsa04136 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04137._colored.png

## 140/345: Finished mitophagy_-_animal id: hsa04137 with 6.122% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04140._colored.png

## 141/345: Finished autophagy_-_animal id: hsa04140 with 4.808% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04141._colored.png

## 142/345: Finished protein_processing_in_endoplasmic_reticulum id: hsa04141 with 6.061% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04142._colored.png

## Info: some node width is different from others, and hence adjusted!

## 143/345: Finished lysosome id: hsa04142 with 15.49% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04144._colored.png

## Info: some node width is different from others, and hence adjusted!

## 144/345: Finished endocytosis id: hsa04144 with 9.167% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04145._colored.png

## 145/345: Finished phagosome id: hsa04145 with 33.78% genes mapped(19 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04146._colored.png

## 146/345: Finished peroxisome id: hsa04146 with 7.692% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04150._colored.png

## 147/345: Finished mtor_signaling_pathway id: hsa04150 with 9.211% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04151._colored.png

## 148/345: Finished pi3k-akt_signaling_pathway id: hsa04151 with 16.67% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04152._colored.png

## 149/345: Finished ampk_signaling_pathway id: hsa04152 with 29.41% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04210._colored.png

## 150/345: Finished apoptosis id: hsa04210 with 16.04% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04211._colored.png

## 151/345: Finished longevity_regulating_pathway id: hsa04211 with 17.78% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04213._colored.png

## Info: some node width is different from others, and hence adjusted!

## 152/345: Finished longevity_regulating_pathway_-_multiple_species id: hsa04213 with 4.082% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04215._colored.png

## Info: some node width is different from others, and hence adjusted!

## 153/345: Finished apoptosis_-_multiple_species id: hsa04215 with 11.11% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04216._colored.png

## 154/345: Finished ferroptosis id: hsa04216 with 26.47% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04217._colored.png

## 155/345: Finished necroptosis id: hsa04217 with 17.11% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04218._colored.png

## 156/345: Finished cellular_senescence id: hsa04218 with 17.53% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04260._colored.png

## 157/345: Finished cardiac_muscle_contraction id: hsa04260 with 40.74% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04261._colored.png

## 158/345: Finished adrenergic_signaling_in_cardiomyocytes id: hsa04261 with 33.33% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04270._colored.png

## 159/345: Finished vascular_smooth_muscle_contraction id: hsa04270 with 20.75% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04310._colored.png

## 160/345: Finished wnt_signaling_pathway id: hsa04310 with 21.69% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04330._colored.png

## 161/345: Finished notch_signaling_pathway id: hsa04330 with 4% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04340._colored.png

## 162/345: Finished hedgehog_signaling_pathway id: hsa04340 with 30.51% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04350._colored.png

## 163/345: Finished tgf-beta_signaling_pathway id: hsa04350 with 13.89% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04360._colored.png

## 164/345: Finished axon_guidance id: hsa04360 with 17.27% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04370._colored.png

## 165/345: Finished vegf_signaling_pathway id: hsa04370 with 17.86% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04371._colored.png

## 166/345: Finished apelin_signaling_pathway id: hsa04371 with 22.58% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04380._colored.png

## 167/345: Finished osteoclast_differentiation id: hsa04380 with 21.13% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04390._colored.png

## 168/345: Finished hippo_signaling_pathway id: hsa04390 with 12.09% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04392._colored.png

## 169/345: Finished hippo_signaling_pathway_-_multiple_species id: hsa04392 with 10% genes mapped(2 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04510._colored.png

## 170/345: Finished focal_adhesion id: hsa04510 with 13.33% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04512._colored.png

## 171/345: Finished ecm-receptor_interaction id: hsa04512 with 32.23% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04514._colored.png

## 172/345: Finished cell_adhesion_molecules id: hsa04514 with 28.63% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04520._colored.png

## 173/345: Finished adherens_junction id: hsa04520 with 12.16% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04530._colored.png

## 174/345: Finished tight_junction id: hsa04530 with 24.62% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04540._colored.png

## 175/345: Finished gap_junction id: hsa04540 with 33.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04550._colored.png

## 176/345: Finished signaling_pathways_regulating_pluripotency_of_stem_cells id: hsa04550 with 18.37% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04610._colored.png

## 177/345: Finished complement_and_coagulation_cascades id: hsa04610 with 23.53% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04611._colored.png

## Info: some node width is different from others, and hence adjusted!

## 178/345: Finished platelet_activation id: hsa04611 with 17.39% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04612._colored.png

## 179/345: Finished antigen_processing_and_presentation id: hsa04612 with 43.59% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04613._colored.png

## 180/345: Finished neutrophil_extracellular_trap_formation id: hsa04613 with 25.88% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04614._colored.png

## 181/345: Finished renin-angiotensin_system id: hsa04614 with 34.48% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04620._colored.png

## 182/345: Finished toll-like_receptor_signaling_pathway id: hsa04620 with 22.78% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04621._colored.png

## Info: some node width is different from others, and hence adjusted!

## 183/345: Finished nod-like_receptor_signaling_pathway id: hsa04621 with 23.03% genes mapped(29 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04622._colored.png

## 184/345: Finished rig-i-like_receptor_signaling_pathway id: hsa04622 with 15.38% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04623._colored.png

## 185/345: Finished cytosolic_dna-sensing_pathway id: hsa04623 with 25.81% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04625._colored.png

## 186/345: Finished c-type_lectin_receptor_signaling_pathway id: hsa04625 with 32.47% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04630._colored.png

## 187/345: Finished jak-stat_signaling_pathway id: hsa04630 with 22.86% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04640._colored.png

## 188/345: Finished hematopoietic_cell_lineage id: hsa04640 with 44.53% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04650._colored.png

## 189/345: Finished natural_killer_cell_mediated_cytotoxicity id: hsa04650 with 36.26% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04657._colored.png

## 190/345: Finished il-17_signaling_pathway id: hsa04657 with 29.67% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04658._colored.png

## Info: some node width is different from others, and hence adjusted!

## 191/345: Finished th1_and_th2_cell_differentiation id: hsa04658 with 21.54% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04659._colored.png

## 192/345: Finished th17_cell_differentiation id: hsa04659 with 23.08% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04660._colored.png

## Info: some node width is different from others, and hence adjusted!

## 193/345: Finished t_cell_receptor_signaling_pathway id: hsa04660 with 12.12% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04662._colored.png

## 194/345: Finished b_cell_receptor_signaling_pathway id: hsa04662 with 8.889% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04664._colored.png

## 195/345: Finished fc_epsilon_ri_signaling_pathway id: hsa04664 with 26.19% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04666._colored.png

## 196/345: Finished fc_gamma_r-mediated_phagocytosis id: hsa04666 with 17.02% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04668._colored.png

## 197/345: Finished tnf_signaling_pathway id: hsa04668 with 28.57% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04670._colored.png

## 198/345: Finished leukocyte_transendothelial_migration id: hsa04670 with 10.13% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04672._colored.png

## 199/345: Finished intestinal_immune_network_for_iga_production id: hsa04672 with 27.78% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04710._colored.png

## 200/345: Finished circadian_rhythm id: hsa04710 with 5.882% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04713._colored.png

## 201/345: Finished circadian_entrainment id: hsa04713 with 45.65% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04714._colored.png

## 202/345: Finished thermogenesis id: hsa04714 with 14.81% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04720._colored.png

## 203/345: Finished long-term_potentiation id: hsa04720 with 16% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04721._colored.png

## 204/345: Finished synaptic_vesicle_cycle id: hsa04721 with 27.59% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04722._colored.png

## 205/345: Finished neurotrophin_signaling_pathway id: hsa04722 with 15.58% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04723._colored.png

## Info: some node width is different from others, and hence adjusted!
## Info: some node width is different from others, and hence adjusted!

## 206/345: Finished retrograde_endocannabinoid_signaling id: hsa04723 with 39.02% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04724._colored.png

## 207/345: Finished glutamatergic_synapse id: hsa04724 with 35.42% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04725._colored.png

## 208/345: Finished cholinergic_synapse id: hsa04725 with 17.5% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04726._colored.png

## 209/345: Finished serotonergic_synapse id: hsa04726 with 29.79% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04727._colored.png

## 210/345: Finished gabaergic_synapse id: hsa04727 with 35.14% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04728._colored.png

## 211/345: Finished dopaminergic_synapse id: hsa04728 with 25% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04730._colored.png

## 212/345: Finished long-term_depression id: hsa04730 with 33.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04740._colored.png

## Info: some node width is different from others, and hence adjusted!

## 213/345: Finished olfactory_transduction id: hsa04740 with 36% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04742._colored.png

## Info: some node width is different from others, and hence adjusted!

## 214/345: Finished taste_transduction id: hsa04742 with 14.71% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04744._colored.png

## 215/345: Finished phototransduction id: hsa04744 with 7.143% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04750._colored.png

## 216/345: Finished inflammatory_mediator_regulation_of_trp_channels id: hsa04750 with 22.45% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04810._colored.png

## 217/345: Finished regulation_of_actin_cytoskeleton id: hsa04810 with 9.211% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04910._colored.png

## 218/345: Finished insulin_signaling_pathway id: hsa04910 with 20.97% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04911._colored.png

## 219/345: Finished insulin_secretion id: hsa04911 with 25.64% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04912._colored.png

## 220/345: Finished gnrh_signaling_pathway id: hsa04912 with 12.2% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04913._colored.png

## 221/345: Finished ovarian_steroidogenesis id: hsa04913 with 26.67% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04914._colored.png

## 222/345: Finished progesterone-mediated_oocyte_maturation id: hsa04914 with 31.58% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04915._colored.png

## 223/345: Finished estrogen_signaling_pathway id: hsa04915 with 22.58% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04916._colored.png

## 224/345: Finished melanogenesis id: hsa04916 with 39.47% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04917._colored.png

## 225/345: Finished prolactin_signaling_pathway id: hsa04917 with 11.11% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04918._colored.png

## 226/345: Finished thyroid_hormone_synthesis id: hsa04918 with 16.67% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04919._colored.png

## 227/345: Finished thyroid_hormone_signaling_pathway id: hsa04919 with 15.38% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04920._colored.png

## 228/345: Finished adipocytokine_signaling_pathway id: hsa04920 with 38.89% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04921._colored.png

## 229/345: Finished oxytocin_signaling_pathway id: hsa04921 with 25.86% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04922._colored.png

## 230/345: Finished glucagon_signaling_pathway id: hsa04922 with 30% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04923._colored.png

## 231/345: Finished regulation_of_lipolysis_in_adipocytes id: hsa04923 with 33.33% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04924._colored.png

## 232/345: Finished renin_secretion id: hsa04924 with 40% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04925._colored.png

## 233/345: Finished aldosterone_synthesis_and_secretion id: hsa04925 with 26.83% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04926._colored.png

## 234/345: Finished relaxin_signaling_pathway id: hsa04926 with 28.4% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04927._colored.png

## 235/345: Finished cortisol_synthesis_and_secretion id: hsa04927 with 24.39% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04928._colored.png

## 236/345: Finished parathyroid_hormone_synthesis,_secretion_and_action id: hsa04928 with 21.21% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04929._colored.png

## 237/345: Finished gnrh_secretion id: hsa04929 with 12.12% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04930._colored.png

## 238/345: Finished type_ii_diabetes_mellitus id: hsa04930 with 36% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04931._colored.png

## 239/345: Finished insulin_resistance id: hsa04931 with 29.29% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04932._colored.png

## 240/345: Finished non-alcoholic_fatty_liver_disease id: hsa04932 with 26.47% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04933._colored.png

## 241/345: Finished age-rage_signaling_pathway_in_diabetic_complications id: hsa04933 with 25.81% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04934._colored.png

## 242/345: Finished cushing_syndrome id: hsa04934 with 21.84% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04935._colored.png

## 243/345: Finished growth_hormone_synthesis,_secretion_and_action id: hsa04935 with 20% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04936._colored.png

## 244/345: Finished alcoholic_liver_disease id: hsa04936 with 23.85% genes mapped(19 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04940._colored.png

## 245/345: Finished type_i_diabetes_mellitus id: hsa04940 with 57.14% genes mapped(11 unique).

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04950._colored.png

## 246/345: Finished maturity_onset_diabetes_of_the_young id: hsa04950 with 0% genes mapped(0 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04960._colored.png

## 247/345: Finished aldosterone-regulated_sodium_reabsorption id: hsa04960 with 21.05% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04961._colored.png

## 248/345: Finished endocrine_and_other_factor-regulated_calcium_reabsorption id: hsa04961 with 22.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04962._colored.png

## 249/345: Finished vasopressin-regulated_water_reabsorption id: hsa04962 with 4.348% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04964._colored.png

## 250/345: Finished proximal_tubule_bicarbonate_reclamation id: hsa04964 with 23.08% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04966._colored.png

## 251/345: Finished collecting_duct_acid_secretion id: hsa04966 with 16.67% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04970._colored.png

## 252/345: Finished salivary_secretion id: hsa04970 with 35% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04971._colored.png

## 253/345: Finished gastric_acid_secretion id: hsa04971 with 36.67% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04972._colored.png

## 254/345: Finished pancreatic_secretion id: hsa04972 with 29.79% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04973._colored.png

## 255/345: Finished carbohydrate_digestion_and_absorption id: hsa04973 with 27.27% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04974._colored.png

## Info: some node width is different from others, and hence adjusted!

## 256/345: Finished protein_digestion_and_absorption id: hsa04974 with 37.04% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04975._colored.png

## 257/345: Finished fat_digestion_and_absorption id: hsa04975 with 15.62% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04976._colored.png

## 258/345: Finished bile_secretion id: hsa04976 with 15.62% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04977._colored.png

## 259/345: Finished vitamin_digestion_and_absorption id: hsa04977 with 2.632% genes mapped(1 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04978._colored.png

## 260/345: Finished mineral_absorption id: hsa04978 with 32.35% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa04979._colored.png

## 261/345: Finished cholesterol_metabolism id: hsa04979 with 16.25% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05010._colored.png

## 262/345: Finished alzheimer_disease id: hsa05010 with 17.29% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05012._colored.png

## 263/345: Finished parkinson_disease id: hsa05012 with 11.65% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05014._colored.png

## 264/345: Finished amyotrophic_lateral_sclerosis id: hsa05014 with 4.286% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05016._colored.png

## 265/345: Finished huntington_disease id: hsa05016 with 10.89% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05017._colored.png

## 266/345: Finished spinocerebellar_ataxia id: hsa05017 with 11.9% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05020._colored.png

## 267/345: Finished prion_disease id: hsa05020 with 13.46% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05022._colored.png

## 268/345: Finished pathways_of_neurodegeneration_-_multiple_diseases id: hsa05022 with 12.4% genes mapped(25 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05030._colored.png

## 269/345: Finished cocaine_addiction id: hsa05030 with 30.61% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05031._colored.png

## 270/345: Finished amphetamine_addiction id: hsa05031 with 32.79% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05032._colored.png

## 271/345: Finished morphine_addiction id: hsa05032 with 27.27% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05033._colored.png

## 272/345: Finished nicotine_addiction id: hsa05033 with 30.77% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05034._colored.png

## 273/345: Finished alcoholism id: hsa05034 with 25.81% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05100._colored.png

## Info: some node width is different from others, and hence adjusted!

## 274/345: Finished bacterial_invasion_of_epithelial_cells id: hsa05100 with 6.818% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05110._colored.png

## 275/345: Finished vibrio_cholerae_infection id: hsa05110 with 17.65% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05120._colored.png

## 276/345: Finished epithelial_cell_signaling_in_helicobacter_pylori_infection id: hsa05120 with 29.41% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05130._colored.png

## 277/345: Finished pathogenic_escherichia_coli_infection id: hsa05130 with 12.17% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05131._colored.png

## 278/345: Finished shigellosis id: hsa05131 with 12.1% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05132._colored.png

## Info: some node width is different from others, and hence adjusted!

## 279/345: Finished salmonella_infection id: hsa05132 with 12.08% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05133._colored.png

## 280/345: Finished pertussis id: hsa05133 with 29.63% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05134._colored.png

## Info: some node width is different from others, and hence adjusted!

## 281/345: Finished legionellosis id: hsa05134 with 28.89% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05135._colored.png

## 282/345: Finished yersinia_infection id: hsa05135 with 11.96% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05140._colored.png

## 283/345: Finished leishmaniasis id: hsa05140 with 30.43% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05142._colored.png

## 284/345: Finished chagas_disease id: hsa05142 with 34.85% genes mapped(18 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05143._colored.png

## 285/345: Finished african_trypanosomiasis id: hsa05143 with 37.93% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05144._colored.png

## 286/345: Finished malaria id: hsa05144 with 43.59% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05145._colored.png

## 287/345: Finished toxoplasmosis id: hsa05145 with 29.31% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05146._colored.png

## 288/345: Finished amoebiasis id: hsa05146 with 47.83% genes mapped(20 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05150._colored.png

## 289/345: Finished staphylococcus_aureus_infection id: hsa05150 with 39.47% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05152._colored.png

## 290/345: Finished tuberculosis id: hsa05152 with 24.53% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05160._colored.png

## 291/345: Finished hepatitis_c id: hsa05160 with 19.78% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05161._colored.png

## Info: some node width is different from others, and hence adjusted!

## 292/345: Finished hepatitis_b id: hsa05161 with 17.83% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05162._colored.png

## 293/345: Finished measles id: hsa05162 with 22.09% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05163._colored.png

## Info: some node width is different from others, and hence adjusted!

## 294/345: Finished human_cytomegalovirus_infection id: hsa05163 with 24.83% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05164._colored.png

## 295/345: Finished influenza_a id: hsa05164 with 21.82% genes mapped(22 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05165._colored.png

## 296/345: Finished human_papillomavirus_infection id: hsa05165 with 17.61% genes mapped(23 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05166._colored.png

## Info: some node width is different from others, and hence adjusted!

## 297/345: Finished human_t-cell_leukemia_virus_1_infection id: hsa05166 with 21.67% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05167._colored.png

## Info: some node width is different from others, and hence adjusted!

## 298/345: Finished kaposi_sarcoma-associated_herpesvirus_infection id: hsa05167 with 23.39% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05168._colored.png

## 299/345: Finished herpes_simplex_virus_1_infection id: hsa05168 with 25.2% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05169._colored.png

## 300/345: Finished epstein-barr_virus_infection id: hsa05169 with 18.94% genes mapped(21 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05170._colored.png

## 301/345: Finished human_immunodeficiency_virus_1_infection id: hsa05170 with 19.01% genes mapped(14 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05171._colored.png

## 302/345: Finished coronavirus_disease_-_covid-19 id: hsa05171 with 40% genes mapped(29 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05200._colored.png

## Info: some node width is different from others, and hence adjusted!

## 303/345: Finished pathways_in_cancer id: hsa05200 with 22.94% genes mapped(53 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05202._colored.png

## 304/345: Finished transcriptional_misregulation_in_cancer id: hsa05202 with 17.79% genes mapped(28 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05203._colored.png

## 305/345: Finished viral_carcinogenesis id: hsa05203 with 15.22% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05204._colored.png

## 306/345: Finished chemical_carcinogenesis_-_dna_adducts id: hsa05204 with 23.68% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05205._colored.png

## 307/345: Finished proteoglycans_in_cancer id: hsa05205 with 11.67% genes mapped(16 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05206._colored.png

## Info: some node width is different from others, and hence adjusted!

## 308/345: Finished micrornas_in_cancer id: hsa05206 with 4.889% genes mapped(17 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05207._colored.png

## 309/345: Finished chemical_carcinogenesis_-_receptor_activation id: hsa05207 with 19.05% genes mapped(18 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05208._colored.png

## 310/345: Finished chemical_carcinogenesis_-_reactive_oxygen_species id: hsa05208 with 16.25% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05210._colored.png

## 311/345: Finished colorectal_cancer id: hsa05210 with 9.722% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05211._colored.png

## 312/345: Finished renal_cell_carcinoma id: hsa05211 with 9.259% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05212._colored.png

## 313/345: Finished pancreatic_cancer id: hsa05212 with 13.46% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05213._colored.png

## 314/345: Finished endometrial_cancer id: hsa05213 with 8.889% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05214._colored.png

## Info: some node width is different from others, and hence adjusted!

## 315/345: Finished glioma id: hsa05214 with 14.06% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05215._colored.png

## 316/345: Finished prostate_cancer id: hsa05215 with 20% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05216._colored.png

## 317/345: Finished thyroid_cancer id: hsa05216 with 15.38% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05217._colored.png

## 318/345: Finished basal_cell_carcinoma id: hsa05217 with 36% genes mapped(8 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05218._colored.png

## 319/345: Finished melanoma id: hsa05218 with 9.375% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05219._colored.png

## Info: some node width is different from others, and hence adjusted!

## 320/345: Finished bladder_cancer id: hsa05219 with 21.88% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05220._colored.png

## 321/345: Finished chronic_myeloid_leukemia id: hsa05220 with 7.843% genes mapped(4 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05221._colored.png

## 322/345: Finished acute_myeloid_leukemia id: hsa05221 with 22.92% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05222._colored.png

## 323/345: Finished small_cell_lung_cancer id: hsa05222 with 13.33% genes mapped(6 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05223._colored.png

## 324/345: Finished non-small_cell_lung_cancer id: hsa05223 with 9.804% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05224._colored.png

## 325/345: Finished breast_cancer id: hsa05224 with 18.27% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05225._colored.png

## 326/345: Finished hepatocellular_carcinoma id: hsa05225 with 11.58% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05226._colored.png

## 327/345: Finished gastric_cancer id: hsa05226 with 14.44% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05230._colored.png

## 328/345: Finished central_carbon_metabolism_in_cancer id: hsa05230 with 18.64% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05231._colored.png

## 329/345: Finished choline_metabolism_in_cancer id: hsa05231 with 12.5% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05235._colored.png

## 330/345: Finished pd-l1_expression_and_pd-1_checkpoint_pathway_in_cancer id: hsa05235 with 12.5% genes mapped(7 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05310._colored.png

## 331/345: Finished asthma id: hsa05310 with 25% genes mapped(5 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05320._colored.png

## 332/345: Finished autoimmune_thyroid_disease id: hsa05320 with 44.74% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05321._colored.png

## 333/345: Finished inflammatory_bowel_disease id: hsa05321 with 36.51% genes mapped(15 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05322._colored.png

## 334/345: Finished systemic_lupus_erythematosus id: hsa05322 with 39.58% genes mapped(13 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05323._colored.png

## 335/345: Finished rheumatoid_arthritis id: hsa05323 with 53.06% genes mapped(24 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05330._colored.png

## 336/345: Finished allograft_rejection id: hsa05330 with 63.33% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05332._colored.png

## 337/345: Finished graft-versus-host_disease id: hsa05332 with 81.82% genes mapped(11 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05340._colored.png

## 338/345: Finished primary_immunodeficiency id: hsa05340 with 6.25% genes mapped(3 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05410._colored.png

## 339/345: Finished hypertrophic_cardiomyopathy id: hsa05410 with 30% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05412._colored.png

## 340/345: Finished arrhythmogenic_right_ventricular_cardiomyopathy id: hsa05412 with 20.34% genes mapped(9 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05414._colored.png

## 341/345: Finished dilated_cardiomyopathy id: hsa05414 with 30% genes mapped(12 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05415._colored.png

## 342/345: Finished diabetic_cardiomyopathy id: hsa05415 with 17.86% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05416._colored.png

## 343/345: Finished viral_myocarditis id: hsa05416 with 29.41% genes mapped(10 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05417._colored.png

## Info: some node width is different from others, and hence adjusted!

## 344/345: Finished lipid_and_atherosclerosis id: hsa05417 with 26.46% genes mapped(27 unique).

## 'select()' returned 1:1 mapping between keys and columns

## Warning: None of the genes or compounds mapped to the pathway!
## Argument gene.idtype or cpd.idtype may be wrong.

## Info: Working in directory /mnt/cbcb/fs01_abelew/cbcb-lab/nelsayed/scratch/atb/rnaseq/lpanamensis_tmrc_2019/tmrc_metabolome

## Info: Writing image file hsa05418._colored.png

## 345/345: Finished fluid_shear_stress_and_atherosclerosis id: hsa05418 with 16.13% genes mapped(13 unique).

pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))
tmp <- sm(saveme(filename=this_save))