L. panamensis 202009: TMRC3 Sample Estimation

1 Introduction

This document is intended to provide an overview of TMRC3 samples which have been sequenced. It includes some plots and analyses showing the relationships among the samples as well as some differential analyses when possible.

2 Annotation

We take the annotation data from ensembl’s biomart instance. The genome which was used to map the data was hg38 revision 91. My default when using biomart is to load the data from 1 year before the current date, which provides annotations which match hg38 91 almost perfectly.

hs_annot <- load_biomart_annotations()

## The biomart annotations file already exists, loading from it.

hs_annot <- hs_annot[["annotation"]]
hs_annot[["transcript"]] <- paste0(rownames(hs_annot), ".", hs_annot[["version"]])
rownames(hs_annot) <- make.names(hs_annot[["ensembl_gene_id"]], unique=TRUE)
tx_gene_map <- hs_annot[, c("transcript", "ensembl_gene_id")]

3 Sample Estimation

I used two mapping methods for this data, hisat2 and salmon. Most analyses use hisat2, which is a more traditional map-and-count method. In contrast, salmon uses what may be thought of as a indexed voting method (so that multi-matches are discounted and the votes split among all matches). Salmon also required a pre-existing database of known transcripts (though later versions may actually use mapping from things like hisat), while hisat uses the genome and a database of known transcripts (and optionally can search for splicing junctions to find new transcripts).

3.1 Generate expressionsets

Caveat: This initial section is using salmon quantifications. A majority of analyses used hisat2.

3.1.1 Salmon expressionsets

Currently, I have these disabled.

hs_expt <- sm(create_expt("sample_sheets/tmrc3_samples_20191001.xlsx",
                          file_column="hg3891salmonfile",
                          gene_info=hs_annot, tx_gene_map=tx_gene_map))

libsizes <- plot_libsize(hs_expt)
libsizes$plot
nonzero <- plot_nonzero(hs_expt)
box <- plot_boxplot(hs_expt)

hs_write <- write_expt(hs_expt, excel=glue("excel/hs_written_salmon-v{ver}.xlsx"))

hs_valid <- subset_expt(hs_expt, coverage=100000)
valid_write <- write_expt(hs_valid, excel=glue("excel/hs_valid_salmon-v{ver}.xlsx"))

3.1.2 Hisat2 expressionsets

The first thing to note is the large range in coverage. There are multiple samples with coverage which is too low to use. These will be removed shortly.

hs_expt <- sm(create_expt("sample_sheets/tmrc3_samples_20200915.xlsx",
                       file_column="hg3891hisatfile",
                       gene_info=hs_annot))

libsizes <- plot_libsize(hs_expt)

## The scale difference between the smallest and largest
## libraries is > 10. Assuming a log10 scale is better, set scale=FALSE if not.

libsizes$plot

nonzero <- plot_nonzero(hs_expt)
nonzero$plot

box <- plot_boxplot(hs_expt)

## This data will benefit from being displayed on the log scale.

## If this is not desired, set scale='raw'

## Some entries are 0.  We are on log scale, adding 1 to the data.

## Changed 2599328 zero count features.

box

3.2 Minimum coverage sample filtering

I arbitrarily chose 3,000,000 counts as a minimal level of coverage. We may want this to be higher.

hs_valid <- subset_expt(hs_expt, coverage=3000000)

## Subsetting given a minimal number of counts/sample.

## There were 69, now there are 63 samples.

plot_libsize(hs_valid)$plot

## The scale difference between the smallest and largest
## libraries is > 10. Assuming a log10 scale is better, set scale=FALSE if not.

valid_write <- sm(write_expt(hs_valid, excel=glue("excel/hs_valid-v{ver}.xlsx")))

## Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

4 Questions from Maria Adelaida

The following comes from an email 20190830 from Maria Adelaida.

1. Samples WT1010 and WT1011 PBMCs from two healthy donors processed 2h, 7h and 12h after sample procurement. This is an analysis to explore the time-effect on gene expression and define steps for data analysis for patient samples considering time-dependent effects.

   1. An initial PCA on the raw data would be very useful to see if there is clustering based on time or (as usual), mostly a donor-specific effect. Then I think a hierarchical clustering of genes based on time-dependent modifications to see what is mostly affected (if any) - like what you guys did for T.cruzi.

2. Samples from SU1017, SU1034 Samples from TMRC CL patients. m= monocyte, n= neutrophil. Samples labeled “1” are taken before treatment and those “2” mid way through treatment. This is exiting, because these will be our first neutrophil transcriptomes.

In an attempt to poke at these questions, I mapped the reads to hg38_91 using salmon and hisat2. It is very noteworthy that the salmon mappings are exhibiting some serious problems and should be looked into further. The hisat2 mappings are significantly more ‘normal’. Having said that, two samples remain basically unusable: tmrc30009 (1034n1) and (to a smaller degree) tmrc30007 (1017n1) have too few reads as shown above.

4.1 Preparation

To address these, I added to the end of the sample sheet columns named ‘condition’, ‘batch’, ‘donor’, and ‘time’. These are filled in with shorthand values according to the above.

4.2 Global view

Before addressing the questions explicitly by subsetting the data, I want to get a look at the samples as they are.

hs_valid <- set_expt_batches(hs_valid, fact="donor")
hs_valid <- set_expt_samplenames(hs_valid, newnames=pData(hs_valid)[["samplename"]])
all_norm <- sm(normalize_expt(hs_valid, transform="log2", convert="cpm", batch="svaseq",
                           filter=TRUE))
all_pca <- plot_pca(all_norm)

## Potentially check over the experimental design, there appear to be missing values.

## Warning in plot_pca(all_norm): There are NA values in the component data. This
## can lead to weird plotting errors.

all_pca$plot

## Warning: Removed 1 rows containing missing values (geom_point).

all_ts <- plot_tsne(all_norm)

## Potentially check over the experimental design, there appear to be missing values.

## Warning in plot_pca(..., pc_method = "tsne"): There are NA values in the
## component data. This can lead to weird plotting errors.

all_ts$plot

## Warning: Removed 1 rows containing missing values (geom_point).

knitr::kable(all_pca$table)

	sampleid	condition	batch	batch_int	colors	labels	PC1	PC2	pc_1	pc_2	pc_3	pc_4	pc_5	pc_6	pc_7	pc_8	pc_9	pc_10	pc_11	pc_12	pc_13	pc_14	pc_15	pc_16	pc_17	pc_18	pc_19	pc_20	pc_21	pc_22	pc_23	pc_24	pc_25	pc_26	pc_27	pc_28	pc_29	pc_30	pc_31	pc_32	pc_33	pc_34	pc_35	pc_36	pc_37	pc_38	pc_39	pc_40	pc_41	pc_42	pc_43	pc_44	pc_45	pc_46	pc_47	pc_48	pc_49	pc_50	pc_51	pc_52	pc_53	pc_54	pc_55	pc_56	pc_57	pc_58	pc_59	pc_60	pc_61
1010-2	1010-2	PBMCs	d1010	1	#1B9E77	1010-2	-0.0815	-0.1544	-0.0815	-0.1544	-0.0748	0.1318	0.0973	-0.1087	0.2378	-0.0297	0.1310	-0.0522	0.0540	-0.1060	0.0624	-0.0768	-0.1116	-0.1929	-0.1450	0.5646	-0.1153	0.2196	-0.2106	0.0649	-0.0340	0.1597	-0.1476	0.1088	-0.0248	-0.1447	0.0277	0.0542	-0.0393	-0.0756	0.2347	0.0794	0.0163	0.1063	0.0041	0.1753	-0.0230	-0.1109	-0.0247	-0.1946	-0.0339	-0.0049	0.1652	0.0262	0.1242	0.0111	0.0608	0.0298	0.0242	0.0092	0.0500	0.0416	0.0327	0.0546	0.0012	0.0115	0.0108	0.0137	0.0461
1010-7	1010-7	PBMCs	d1010	1	#1B9E77	1010-7	-0.0441	-0.1633	-0.0441	-0.1633	-0.0469	0.0388	0.0836	-0.0282	0.3063	-0.1100	0.1234	0.0401	-0.0323	0.0198	0.0235	-0.0628	0.0502	-0.0457	-0.0967	-0.0969	-0.0231	0.0309	0.1133	-0.2092	-0.2037	-0.0133	-0.1168	0.1333	-0.1249	0.0228	-0.1067	-0.0450	0.1901	0.0299	-0.0900	-0.1474	-0.0474	-0.0946	0.0277	0.0015	-0.0175	-0.1107	0.1529	0.0055	0.0340	0.0127	-0.1667	0.1469	-0.0591	0.2241	-0.4415	-0.2394	-0.0264	0.3245	-0.0368	-0.0585	-0.1405	-0.1406	0.0078	0.0911	-0.0345	-0.0038	-0.0043
1010-12	1010-12	PBMCs	d1010	1	#1B9E77	1010-12	0.0029	-0.2256	0.0029	-0.2256	-0.0603	0.0572	-0.0338	-0.1090	0.3648	-0.0841	0.1395	0.0539	0.0816	-0.1512	-0.0264	-0.1028	0.2509	-0.0196	-0.0858	-0.0845	0.0098	0.0152	-0.0903	-0.0290	0.1014	-0.0102	0.1939	0.0650	0.1107	-0.0501	0.0442	0.0457	0.1061	0.2105	-0.0500	-0.3319	0.0461	-0.1387	-0.0205	-0.2138	0.1897	0.0746	0.0016	0.1041	-0.1439	-0.0449	-0.0255	0.0250	-0.1918	0.0096	0.3141	0.0485	0.0337	-0.2313	-0.0637	-0.0282	0.1150	0.0835	-0.0567	-0.1330	0.0246	0.0062	-0.0227
1011-2	1011-2	PBMCs	d1011	2	#1B9E77	1011-2	0.0020	-0.0908	0.0020	-0.0908	-0.0849	0.0228	-0.0335	-0.0322	0.0943	-0.1369	-0.0010	0.0560	-0.0700	0.0058	-0.0324	-0.0293	-0.0223	0.0347	0.1653	0.1179	0.0488	0.0090	-0.0271	0.1260	-0.0218	0.0250	0.0723	-0.0187	0.0940	0.0991	0.0766	-0.0611	-0.0995	-0.1969	0.1620	0.1418	0.1783	0.1603	-0.0245	-0.0794	-0.0417	0.2942	0.0333	0.1742	0.2405	-0.0722	-0.0588	-0.0697	-0.2417	-0.1732	-0.0496	-0.2371	-0.0126	-0.0191	-0.2320	-0.2596	0.0532	-0.1025	-0.3387	0.2793	-0.0133	-0.0413	-0.0644
1011-7	1011-7	PBMCs	d1011	2	#1B9E77	1011-7	-0.0111	-0.0791	-0.0111	-0.0791	-0.1119	0.0423	-0.0377	-0.0270	0.1733	-0.1302	0.0401	0.1277	-0.0694	0.0118	0.0238	-0.0272	0.0558	0.0867	0.1598	-0.0096	0.0377	-0.0473	0.0665	0.0994	-0.0361	-0.1164	0.0437	0.0032	0.1836	0.1424	0.0578	0.0217	-0.1053	-0.0073	0.0848	0.1268	-0.0099	0.1419	-0.0318	0.0428	-0.0982	0.0626	0.0156	0.0040	0.0558	0.0554	0.1457	-0.0131	-0.0714	-0.2134	-0.0528	-0.0356	-0.0745	0.0602	-0.0728	0.1595	-0.3595	-0.1153	0.3925	-0.5116	0.0439	0.0778	-0.0383
1011-12	1011-12	PBMCs	d1011	2	#1B9E77	1011-12	-0.0148	-0.1066	-0.0148	-0.1066	-0.1148	0.0404	-0.0657	-0.0397	0.2810	-0.1550	0.1014	0.2349	-0.1175	-0.0154	0.0904	-0.0664	0.0917	0.1146	0.1462	-0.2523	0.0697	-0.0846	0.0714	0.0417	-0.0792	-0.1975	0.0444	0.0321	-0.0412	0.1714	0.0189	-0.0390	-0.1346	-0.0300	-0.0683	0.1717	-0.1532	0.1099	0.0167	0.2316	-0.0860	-0.1536	-0.1487	-0.0225	-0.0483	0.0161	0.1267	-0.0692	0.2237	0.0480	0.0366	0.2874	0.0312	-0.0440	0.1922	0.0182	0.1478	0.1172	-0.0942	0.3204	-0.0485	-0.0478	0.0472
1034n1	1034n1	Neutrophils	d1034	3	#D95F02	1034n1	-0.3559	0.1381	-0.3559	0.1381	0.3661	0.0420	-0.0376	-0.2519	-0.0075	0.0226	0.0326	0.2228	-0.0091	-0.1689	-0.3867	0.0183	-0.0095	-0.1266	0.3581	0.0288	0.1035	-0.0737	-0.1673	-0.2038	0.0955	0.1673	-0.1792	0.0019	-0.0586	0.1088	0.0419	0.0357	0.1554	-0.0015	-0.0213	0.0136	-0.0939	-0.0841	-0.0491	0.0145	-0.0433	0.0331	-0.1430	0.0730	-0.0357	0.0588	0.0417	0.0147	-0.0048	-0.0434	-0.0686	0.0134	0.0055	-0.0442	0.0211	-0.0164	-0.0039	-0.0301	0.0079	-0.0182	-0.0039	-0.0005	-0.0023
1034bp1	1034bp1	Biopsy	NA	NA	#E7298A	1034bp1	-0.0069	-0.0068	-0.0069	-0.0068	-0.1001	-0.0395	0.0378	-0.0693	-0.1596	0.0624	-0.0425	0.0190	-0.0223	0.0344	0.0900	0.0470	0.1525	0.1454	0.0506	0.0066	-0.0059	0.0090	0.0307	0.0378	0.0495	-0.1124	-0.2335	-0.0847	0.0800	-0.0484	-0.0873	0.1307	-0.0910	0.0975	0.1167	-0.2775	0.0533	-0.1311	-0.1333	0.1015	0.1721	-0.1719	-0.1208	-0.0169	0.2324	-0.0402	0.3098	0.2899	-0.1393	-0.2031	-0.1177	-0.0221	0.1465	-0.0358	0.3357	-0.1265	-0.0167	-0.1872	-0.1516	0.0022	0.0819	-0.0638	-0.0355
1034n2	1034n2	Neutrophils	d1034	3	#D95F02	1034n2	-0.3230	0.1389	-0.3230	0.1389	0.3137	-0.1296	-0.0489	-0.3239	0.1652	0.2292	-0.4298	-0.0600	-0.0581	0.0832	0.1443	-0.3582	0.0380	0.0682	-0.1046	-0.0538	-0.0728	0.0576	0.1238	0.2180	-0.0310	-0.2034	0.0686	0.1079	-0.0082	-0.0998	0.0171	-0.0299	-0.0781	-0.0094	0.0508	-0.0004	0.0823	0.0721	0.0509	-0.0566	0.0078	-0.0237	0.0912	-0.0622	0.0301	0.0011	-0.0309	0.0233	0.0088	0.0613	0.0325	-0.0247	-0.0084	0.0219	-0.0186	0.0147	-0.0154	0.0217	-0.0072	0.0097	0.0072	-0.0010	-0.0003
1034m2	1034m2	Monocytes	d1034	3	#7570B3	1034m2	-0.1326	-0.0061	-0.1326	-0.0061	0.0821	-0.0059	0.1444	0.0127	-0.1540	-0.2156	-0.0756	0.0146	0.0306	0.0829	0.2125	0.0504	0.0310	0.0450	-0.1632	0.0524	-0.0445	0.1358	0.0133	0.0163	-0.0958	0.0547	0.2520	-0.0411	-0.0509	0.0725	-0.0846	0.0366	0.3124	-0.2324	0.0430	0.0531	0.0364	0.0887	0.1443	-0.0903	0.1645	0.0291	-0.4025	0.2590	-0.3319	-0.0048	0.0595	-0.0222	-0.0624	-0.0719	-0.1460	0.1354	-0.0168	-0.0117	0.1297	-0.0337	-0.1477	-0.0647	-0.0248	-0.0018	0.0025	0.0275	-0.0087
1034m2-	1034m2-	Monocytes	d1034	3	#7570B3	1034m2-	-0.2257	0.0210	-0.2257	0.0210	0.2731	0.1140	0.3021	-0.1255	-0.3034	-0.4326	0.2012	0.1919	0.1697	-0.1159	0.1996	0.1538	-0.0664	-0.0156	-0.1980	-0.0919	-0.0964	-0.0639	0.0225	0.0874	-0.0475	-0.0668	0.0356	-0.0782	0.0119	-0.0006	0.0114	-0.1121	-0.2374	0.1260	-0.0666	-0.0701	0.0041	0.0152	-0.0640	0.0088	-0.0602	-0.0169	0.1963	-0.0860	0.1083	-0.0362	-0.0238	-0.0205	0.0207	-0.0005	0.0952	-0.0730	0.0197	0.0072	-0.0784	0.0054	0.0458	0.0370	0.0036	-0.0092	-0.0085	-0.0032	0.0154
2050bp1	2050bp1	Biopsy	d2050	4	#E7298A	2050bp1	-0.0728	-0.0178	-0.0728	-0.0178	-0.1274	-0.0117	-0.0031	0.0045	-0.0382	0.0118	-0.0519	0.0986	-0.0613	0.1342	0.1271	-0.0577	-0.0185	0.1349	-0.0169	0.0844	-0.1152	0.1626	-0.0462	-0.1063	0.1009	-0.0665	-0.1843	-0.1178	-0.1681	0.0928	-0.1357	0.0714	0.1119	-0.1095	-0.2015	-0.0734	-0.1522	-0.0475	-0.1352	0.0691	-0.0452	0.1427	-0.1341	-0.0107	0.1530	-0.1671	-0.1585	0.1456	-0.0937	-0.0998	0.2580	-0.1842	-0.2365	-0.1245	-0.0641	0.1399	-0.1041	0.2714	0.2918	0.2513	-0.0013	0.0150	-0.0215
2052bp1	2052bp1	Biopsy	d2052	5	#E7298A	2052bp1	0.0413	-0.0787	0.0413	-0.0787	-0.0912	-0.0127	0.0159	-0.2144	-0.1036	0.1734	0.1115	0.0004	-0.1156	-0.1598	-0.0406	0.1476	-0.1280	0.1521	0.0956	-0.1316	-0.1269	0.2361	0.1606	0.0813	0.1096	0.2486	0.1977	0.2473	0.1046	0.0055	-0.0921	-0.3114	0.0474	-0.4273	-0.1769	-0.0278	0.0817	-0.1021	-0.1889	-0.0313	-0.0056	-0.0795	0.1399	-0.0789	0.0215	0.0217	0.0982	0.1134	0.0029	0.0469	0.0009	0.0682	0.0242	-0.0393	0.0209	0.0535	0.0553	0.0010	0.0224	-0.0518	-0.0061	0.0219	0.0006
2052e1	2052e1	Eosinophils	d2052	5	#66A61E	2052e1	0.0044	-0.0473	0.0044	-0.0473	-0.1021	0.0533	-0.0126	-0.0448	-0.0600	-0.0068	-0.1188	-0.0834	0.0500	-0.1470	-0.0830	0.0794	0.0493	0.0964	0.1383	0.1782	-0.0724	-0.0585	-0.0176	0.0339	0.1722	-0.1560	0.2553	-0.1458	-0.2142	-0.0455	0.2348	-0.0584	-0.1049	0.0309	-0.2159	0.2033	-0.0482	-0.1006	0.1896	0.2720	0.1719	-0.3676	-0.0828	-0.0734	-0.1215	0.0608	-0.1746	0.0940	-0.2195	0.0382	0.0002	-0.2087	0.0327	0.0188	-0.1185	-0.0926	0.0349	-0.0621	0.0145	-0.0521	0.0131	0.0148	-0.0466
2052n2	2052n2	Neutrophils	d2052	5	#D95F02	2052n2	-0.0818	0.0927	-0.0818	0.0927	0.0105	-0.3979	-0.0508	0.1484	-0.0969	-0.0531	0.3625	-0.3505	0.0149	-0.2231	0.2551	-0.3739	-0.0118	-0.1245	0.3604	-0.0547	-0.1166	0.0388	-0.0886	-0.0237	-0.1061	-0.0180	0.0542	-0.1493	0.1075	-0.0578	-0.0525	-0.0701	0.0145	-0.0082	0.0090	-0.0278	-0.0894	-0.0309	0.0489	-0.0557	-0.0272	-0.0451	-0.0674	-0.0149	0.0384	0.0570	-0.0202	0.0212	0.0382	-0.0008	0.0002	-0.0441	-0.0184	-0.0016	-0.0208	0.0090	0.0005	0.0084	-0.0017	-0.0020	-0.0009	-0.0011	0.0054
2065bp1	2065bp1	Biopsy	d2065	6	#E7298A	2065bp1	-0.0073	-0.0968	-0.0073	-0.0968	-0.0972	-0.0547	0.0786	-0.2727	-0.1011	0.1435	0.0528	-0.1687	-0.0132	-0.1001	0.1349	0.0139	-0.1856	0.4736	-0.1573	0.0088	0.4528	-0.2468	-0.3028	-0.2055	-0.1844	0.0276	-0.0194	0.0845	0.0633	-0.0157	0.0427	0.0490	-0.0092	0.0050	0.0436	0.0436	-0.0731	-0.0536	0.0752	-0.0666	0.0199	0.0247	0.0084	-0.0571	-0.0341	0.0922	-0.0401	-0.0470	0.0330	-0.0703	0.0112	-0.0145	-0.0763	0.0252	-0.0472	0.0153	-0.0082	0.0256	-0.0053	0.0218	-0.0070	0.0003	0.0139
2066bp1	2066bp1	Biopsy	d2066	7	#E7298A	2066bp1	-0.0164	-0.0524	-0.0164	-0.0524	-0.1225	-0.0403	0.0474	-0.1351	-0.1421	0.1507	0.0522	0.0217	-0.0251	0.0479	0.0599	0.0344	0.0596	-0.0097	0.0334	0.0535	0.1169	0.1162	-0.0301	0.1049	0.0338	-0.0717	-0.0878	-0.0707	0.0569	-0.0504	-0.0859	0.0865	-0.0294	0.0939	0.0178	0.0047	-0.0880	0.2118	-0.4407	0.0540	-0.1084	-0.0737	-0.1936	0.2000	-0.0195	-0.1443	-0.2867	-0.1848	-0.0320	0.4002	-0.0492	0.1249	0.2434	0.0372	-0.1553	-0.1010	0.0430	-0.0417	0.0067	-0.1710	-0.0114	0.0224	-0.0642
2068m1	2068m1	Monocytes	d2068	8	#7570B3	2068m1	0.0261	-0.1464	0.0261	-0.1464	0.0207	0.0213	0.0348	-0.0719	-0.0741	-0.1224	-0.0343	-0.1894	-0.0042	0.0360	-0.2168	0.0673	0.0410	-0.0183	0.1699	0.1769	-0.0074	-0.0791	0.0423	0.1748	-0.1294	-0.0831	0.1512	0.0812	0.0652	-0.1726	0.0388	0.1103	-0.0335	0.1237	-0.2735	-0.0129	0.0711	-0.0737	-0.0561	-0.0066	0.3043	0.3479	-0.0976	-0.1154	0.2030	-0.1405	-0.0440	-0.0159	0.2775	0.1350	-0.1769	0.1665	-0.2438	0.0319	0.1136	0.0154	-0.0438	0.0068	0.0722	0.0538	-0.0079	-0.0088	-0.0020
2068n1	2068n1	Neutrophils	d2068	8	#D95F02	2068n1	-0.0705	0.1074	-0.0705	0.1074	-0.0387	-0.1325	-0.0990	0.1263	0.0119	0.0042	0.0288	0.0883	0.0572	-0.0286	-0.2813	0.0863	-0.0103	0.0145	-0.1241	0.0039	0.0245	-0.0639	-0.1033	0.1605	-0.1654	0.0206	-0.0128	0.0182	0.1162	-0.1847	-0.0493	0.0191	0.0874	-0.1185	-0.1221	-0.1847	-0.0980	0.3262	0.2271	-0.1050	0.0476	-0.3478	0.0092	0.0476	0.2510	-0.2078	-0.0110	-0.1390	-0.2170	-0.1363	-0.0476	0.1317	-0.0211	0.0908	-0.0609	0.2233	0.1580	0.0161	0.0937	0.0680	-0.0294	0.0153	0.0020
2068e1	2068e1	Eosinophils	d2068	8	#66A61E	2068e1	-0.0492	0.0136	-0.0492	0.0136	-0.1157	0.1293	-0.0687	0.0784	0.0218	-0.0307	-0.1387	0.0037	0.0904	-0.1797	0.0058	-0.0282	-0.2163	-0.1888	-0.0462	-0.2386	-0.0496	-0.1903	-0.1633	0.2245	-0.0778	0.0063	-0.0091	0.0294	0.0722	-0.1235	-0.3821	0.3231	0.0839	-0.0697	-0.0434	0.2617	0.0875	-0.2154	-0.0775	0.1662	0.0323	0.0426	0.1188	0.0381	0.0065	0.1393	-0.0717	0.0465	-0.1771	-0.0321	-0.0664	0.0393	0.1342	-0.0577	0.0307	-0.0388	-0.0771	0.2403	-0.0312	-0.0325	0.0069	0.0149	0.0086
2068bp1	2068bp1	Biopsy	d2068	8	#E7298A	2068bp1	0.0037	-0.0540	0.0037	-0.0540	-0.1529	-0.0204	0.0616	-0.1976	-0.1431	0.2948	0.1944	0.1403	-0.0415	0.1894	-0.0275	0.1169	-0.0844	-0.4133	-0.0161	-0.1939	0.1542	0.3761	-0.1136	0.1497	-0.0290	-0.2449	0.0888	-0.0857	-0.0429	0.1134	0.1112	0.1362	-0.0311	0.0456	0.0407	-0.0157	-0.0929	-0.0960	0.1955	-0.0993	0.0831	0.0287	0.0649	-0.0872	-0.0402	0.1253	-0.0138	-0.0572	0.0349	-0.1476	-0.0435	-0.0423	-0.1127	0.0587	-0.0256	0.0177	0.0004	-0.0076	-0.0465	0.0330	-0.0083	-0.0043	0.0362
2072n1	2072n1	Neutrophils	d2072	10	#D95F02	2072n1	-0.0487	0.0659	-0.0487	0.0659	-0.0973	-0.1115	-0.0723	0.1332	-0.0348	-0.0427	0.0542	0.1570	-0.0201	0.0834	-0.1759	0.0002	-0.0207	0.1124	-0.0133	-0.0606	-0.0500	-0.0859	-0.0673	0.2286	-0.1209	0.0959	-0.1493	0.0094	-0.0594	-0.1216	0.1993	0.0405	-0.0574	-0.2276	-0.0128	-0.1435	-0.1321	0.0567	0.0667	-0.0317	0.0173	-0.0047	0.0806	0.0381	-0.1623	0.0102	-0.1071	0.1024	0.2230	0.1788	0.2931	-0.1604	-0.0571	0.0454	0.1754	-0.2495	-0.3547	0.0681	-0.2443	-0.1660	0.0523	-0.0581	0.0020
2072e1	2072e1	Eosinophils	d2072	10	#66A61E	2072e1	0.0037	-0.0938	0.0037	-0.0938	-0.0851	0.0394	0.0042	-0.1087	0.0322	-0.0827	-0.0865	-0.2917	0.1611	-0.0378	-0.2735	-0.0313	-0.3111	-0.0061	-0.1474	-0.2825	-0.3014	0.0645	0.0106	-0.3360	0.1616	-0.2213	-0.1710	-0.1299	0.1986	0.0281	0.1552	0.0366	-0.1176	-0.1105	0.0414	-0.0337	0.0560	0.2120	-0.0329	0.0212	0.1231	0.0316	-0.0655	0.1360	-0.0817	-0.0053	0.0850	-0.0610	0.1137	0.0167	-0.0293	-0.0621	0.0456	0.0012	-0.0029	0.0183	-0.0037	0.0091	0.0293	0.0294	-0.0136	-0.0205	0.0024
2072bp1	2072bp1	Biopsy	d2072	10	#E7298A	2072bp1	0.0352	-0.0262	0.0352	-0.0262	-0.0850	-0.0140	0.0495	-0.1259	-0.0321	0.1156	0.0651	0.0128	0.0626	-0.0192	-0.0258	0.0381	0.0906	0.0402	0.0606	-0.0127	-0.0822	-0.0898	0.2665	0.1278	0.0437	0.2151	-0.0293	-0.0378	0.0616	-0.2442	0.0204	-0.0750	0.2021	0.3502	0.0455	0.1056	0.0581	0.1106	-0.1556	0.0006	0.0410	-0.0810	0.0594	0.1157	-0.1738	0.1621	-0.0532	-0.2560	0.1155	-0.2829	0.0656	-0.2392	0.0387	0.0785	0.1196	0.1624	-0.1785	0.0348	0.0373	0.2990	-0.0246	-0.0259	-0.0240
2071bp1	2071bp1	Biopsy	d2071	9	#E7298A	2071bp1	-0.0291	-0.0098	-0.0291	-0.0098	-0.1418	-0.0421	0.0721	-0.0908	-0.1146	0.2344	0.1140	0.1096	0.0705	0.2720	0.0580	-0.1233	0.1222	-0.3337	-0.1135	0.1821	-0.1757	-0.6264	0.0560	-0.2003	0.0618	-0.0398	0.1160	0.1074	0.0811	0.1196	-0.0206	-0.1032	-0.0578	-0.2118	-0.0285	-0.0202	-0.0087	-0.0107	-0.0404	-0.0095	0.0378	-0.0118	-0.0213	0.0102	0.0211	0.0121	0.0031	-0.0036	0.0017	-0.0075	0.0090	0.0312	-0.0011	-0.0279	-0.0061	-0.0067	0.0031	0.0079	-0.0026	-0.0046	0.0048	-0.0014	-0.0018
2073m1	2073m1	Monocytes	d2073	11	#7570B3	2073m1	-0.0063	0.0209	-0.0063	0.0209	-0.0762	0.0015	-0.0088	0.0519	-0.0734	-0.0845	-0.0898	0.0664	0.0123	0.1132	-0.0198	0.0046	0.0299	0.0747	0.0892	0.0424	-0.0085	0.0147	-0.0181	-0.0195	0.0437	0.0074	0.0635	-0.0124	0.0997	-0.0024	0.0538	0.0440	0.0909	0.0311	0.0930	0.0013	0.0113	-0.0091	0.0352	-0.0790	-0.0222	0.0281	0.0275	-0.0284	0.0465	0.1310	0.0095	0.0993	0.0140	0.1604	-0.0036	-0.0522	0.1469	-0.0075	-0.0644	0.1386	0.0569	0.0091	0.0219	0.0407	0.0420	-0.0310	0.5089
2073e1	2073e1	Eosinophils	d2073	11	#66A61E	2073e1	-0.0675	-0.0011	-0.0675	-0.0011	-0.1104	0.0757	-0.0475	0.0637	-0.0543	-0.0246	-0.1180	0.0430	0.0268	-0.0075	0.0237	-0.0241	-0.0150	-0.0109	0.0287	-0.0191	-0.0584	-0.0398	-0.0159	0.0122	0.0523	0.0097	-0.0493	-0.0278	0.2266	-0.0313	-0.1099	0.2101	0.0376	0.0612	-0.1564	0.1490	0.0293	-0.0786	-0.0609	-0.2584	-0.2837	-0.1200	0.0006	-0.2261	-0.3027	-0.2149	0.1591	0.0244	0.0270	0.0476	0.1369	-0.0336	-0.3069	0.0977	-0.0699	-0.1257	0.1416	-0.4406	0.0093	0.1008	-0.0347	-0.0037	-0.0234
2073bp1	2073bp1	Biopsy	d2073	11	#E7298A	2073bp1	0.0129	-0.0217	0.0129	-0.0217	-0.1156	-0.0330	0.0345	-0.1252	-0.0952	0.1658	0.1217	0.0368	-0.0163	0.0001	-0.0546	-0.0305	-0.0300	-0.0123	0.0021	-0.1202	-0.0169	-0.0324	0.0348	-0.0736	-0.1401	0.1184	0.0143	-0.1361	-0.2190	-0.0971	-0.0107	-0.0882	0.0720	0.2332	-0.0187	0.1421	0.3612	0.1726	0.3452	0.1411	-0.2185	0.1715	0.0583	0.1282	0.0168	-0.3128	0.1940	0.2194	-0.0756	0.2034	0.0518	0.0268	0.0511	-0.1411	0.0763	-0.0395	-0.0002	0.0221	0.0953	-0.0625	0.0022	0.0028	-0.0046
2068m2	2068m2	Monocytes	d2068	8	#7570B3	2068m2	0.0346	-0.0935	0.0346	-0.0935	0.0733	-0.0398	0.0144	0.0368	-0.1413	-0.1589	-0.0604	-0.1174	-0.0189	0.2597	-0.0488	-0.0079	0.0574	-0.0897	0.0774	-0.0611	0.0474	0.1117	0.0765	-0.1112	-0.2110	0.0627	-0.2154	0.2608	0.1304	-0.0073	0.1229	-0.1198	-0.0339	0.0435	0.1705	0.1564	0.0586	-0.0963	-0.0261	0.1214	0.0415	-0.1667	0.0749	0.0454	-0.0166	0.1217	-0.1233	-0.1393	-0.3698	0.1353	0.1196	0.0714	-0.3386	-0.1920	0.2127	-0.0491	0.1079	0.0491	0.0759	-0.0337	0.0506	-0.0235	-0.0106
2068n2	2068n2	Neutrophils	d2068	8	#D95F02	2068n2	-0.0645	0.1292	-0.0645	0.1292	0.0031	-0.1509	-0.0635	0.0907	0.0253	-0.0204	0.0229	0.0445	0.0966	-0.0702	-0.0969	0.0542	0.0060	-0.0418	-0.1601	0.1308	0.2465	0.1632	0.2234	-0.2134	0.1584	-0.1431	0.0731	0.1038	0.2338	0.0080	-0.2357	-0.1481	0.0246	0.0799	0.0552	0.2445	-0.0391	-0.2437	0.1312	0.1136	0.0800	-0.0029	-0.0469	0.1333	0.1779	-0.1962	0.0339	-0.0268	0.1115	0.0210	0.2769	-0.0088	0.0380	0.2883	0.0053	-0.0484	-0.1315	0.0520	-0.1314	-0.0565	-0.0143	-0.0098	0.0173
2068e2	2068e2	Eosinophils	d2068	8	#66A61E	2068e2	-0.0547	0.0328	-0.0547	0.0328	-0.0799	0.1464	-0.0634	0.0927	-0.0469	-0.0011	-0.1804	-0.0371	0.0638	-0.1677	0.2148	-0.0669	-0.0601	-0.2670	-0.0115	-0.0888	0.3514	0.0238	0.3616	-0.1032	0.0123	0.3321	-0.0129	0.0451	0.1491	0.0115	0.3117	0.1473	-0.0989	-0.0442	-0.1266	-0.1736	-0.0244	0.1402	0.0609	0.0920	-0.0353	0.0481	-0.1471	-0.1746	0.0128	-0.0869	-0.1500	0.1290	-0.0136	-0.0800	-0.0415	0.0024	0.0863	-0.0367	0.0060	0.0016	-0.0296	0.0766	-0.0061	0.0106	-0.0348	0.0201	-0.0015
2072m2	2072m2	Monocytes	d2072	10	#7570B3	2072m2	0.2058	-0.3683	0.2058	-0.3683	0.3274	-0.0801	-0.2565	0.0853	-0.0676	0.1486	0.0028	0.1434	0.0596	-0.0748	0.0402	0.0731	-0.4057	0.0373	0.0956	0.2270	-0.0837	-0.0773	0.2875	0.0441	-0.2594	-0.1641	-0.0598	-0.0147	-0.0142	0.2184	-0.0608	0.0613	0.0764	0.0953	0.0153	-0.0987	-0.0273	0.0102	0.0176	-0.0751	0.0366	-0.0373	-0.0098	0.0026	-0.1008	0.0084	0.0069	0.0615	-0.0366	-0.0079	0.1017	0.0031	0.1023	-0.0261	-0.0564	-0.0011	0.0396	0.0239	-0.0313	-0.0180	-0.0147	-0.0127	-0.0011
2072n2	2072n2	Neutrophils	d2072	10	#D95F02	2072n2	-0.0106	0.1271	-0.0106	0.1271	-0.0381	-0.1506	-0.0487	0.1296	-0.0041	-0.0245	0.1157	0.0724	0.0481	-0.0331	-0.1474	-0.1704	-0.0056	0.0524	-0.2222	0.0677	0.1144	0.0157	0.1560	0.1236	-0.0843	0.0002	-0.0521	-0.0160	-0.1500	-0.0799	0.2588	0.0428	-0.1919	-0.0974	0.1024	0.1353	-0.0923	-0.3559	-0.2049	-0.0638	0.0570	0.0598	0.1137	0.2649	-0.2004	-0.1722	0.1039	0.1052	0.0430	-0.0735	-0.2263	0.0069	0.0747	-0.1564	-0.0978	0.0964	0.1675	-0.0424	0.2205	0.0835	-0.0524	-0.0136	-0.0015
2072e2	2072e2	Eosinophils	d2072	10	#66A61E	2072e2	-0.0090	-0.0134	-0.0090	-0.0134	-0.1164	0.0867	-0.0292	0.0025	-0.0088	-0.0393	-0.1301	-0.0439	0.0426	-0.1986	0.0001	0.0324	-0.0101	-0.0502	0.0750	0.1041	0.0026	0.0069	-0.0321	-0.1072	0.0155	-0.1449	0.0473	-0.1090	-0.2042	0.0501	0.0088	-0.0389	-0.0316	-0.1104	0.1660	-0.1320	0.2220	-0.1552	0.0233	-0.1416	-0.2170	-0.0881	0.2010	0.0806	0.0867	-0.0608	-0.4057	-0.0993	0.1012	-0.1005	0.0686	0.3217	0.0342	-0.0867	0.2345	0.1674	-0.2167	-0.2552	0.0077	0.0827	0.0438	-0.0748	0.0081
2073m2	2073m2	Monocytes	d2073	11	#7570B3	2073m2	0.0860	-0.2537	0.0860	-0.2537	0.1578	-0.0342	-0.0692	-0.0183	-0.0609	-0.0559	-0.0153	-0.1777	0.0945	0.0608	-0.1401	0.0081	0.4278	-0.0745	-0.0404	-0.0977	0.1836	0.0267	-0.0120	0.0090	-0.0425	0.0980	-0.2185	-0.1409	-0.1454	0.0752	-0.2980	-0.0757	-0.1790	-0.1839	-0.0171	0.2136	0.0825	0.1626	0.0158	-0.1746	0.1604	-0.0127	0.0223	-0.1931	-0.1141	0.0297	-0.0876	0.1792	0.1023	-0.1098	0.0917	-0.0208	0.1769	0.0340	-0.0942	0.0615	0.0228	-0.0035	0.0515	-0.0100	-0.0018	-0.0499	0.0101
2073n2	2073n2	Neutrophils	d2073	11	#D95F02	2073n2	-0.0398	0.0003	-0.0398	0.0003	-0.1062	-0.0169	-0.0014	0.0140	0.0251	-0.0899	-0.0323	0.1347	-0.0243	0.1170	0.0407	-0.0446	-0.0633	0.0960	0.0280	-0.0384	-0.0374	-0.0176	0.1172	-0.0432	0.0484	0.0183	-0.0494	-0.0844	-0.0824	-0.1089	-0.0773	0.0170	0.2336	-0.0407	0.1280	0.0019	0.1040	-0.0147	0.0589	0.0849	0.0148	0.0077	-0.0307	-0.0305	0.0969	0.0575	-0.2541	-0.0081	0.3430	-0.2099	-0.0590	-0.1218	-0.1173	-0.0435	0.0165	-0.0218	0.5373	0.0012	-0.0850	-0.4088	-0.1039	-0.0306	-0.0999
2073e2	2073e2	Eosinophils	d2073	11	#66A61E	2073e2	-0.0715	-0.0203	-0.0715	-0.0203	-0.1260	0.0714	-0.0232	0.0425	0.0145	0.0276	-0.0890	0.0382	-0.0099	0.0523	0.1564	-0.0490	-0.0476	0.0196	-0.0205	0.1055	-0.1127	0.1018	0.0359	-0.0687	0.0032	0.0765	-0.3070	0.0205	-0.0894	-0.1489	-0.0366	-0.1637	-0.1209	0.0915	-0.4422	0.1004	-0.2498	-0.0303	0.2105	-0.1218	0.0400	0.2077	0.0663	0.1782	0.0789	0.2792	0.0857	-0.1709	-0.0522	-0.0609	0.0033	0.2039	0.1570	-0.0943	-0.0569	-0.0182	0.0178	-0.2212	-0.1122	-0.1073	0.0412	-0.0126	0.0080
2068m3	2068m3	Monocytes	d2068	8	#7570B3	2068m3	0.0511	-0.0587	0.0511	-0.0587	0.0599	-0.0265	-0.0112	0.0345	-0.0768	-0.1442	-0.0851	-0.2136	-0.0236	0.3067	-0.1064	-0.0282	-0.0046	-0.0605	0.0269	-0.0738	-0.0171	0.0503	-0.1288	-0.1147	-0.1564	-0.0690	0.1672	0.2347	-0.1816	-0.1246	0.1491	-0.0025	0.1805	0.0825	-0.1169	-0.0537	-0.0443	-0.0599	-0.2223	0.1536	-0.2989	-0.0585	0.0075	-0.0592	0.0075	-0.0905	0.1301	0.0711	0.0445	-0.3248	0.1078	0.1143	0.2264	0.0593	-0.2326	-0.0026	-0.1016	0.0241	-0.1905	-0.0576	-0.0846	0.0087	-0.0300
2068n3	2068n3	Neutrophils	d2068	8	#D95F02	2068n3	-0.0342	0.1428	-0.0342	0.1428	-0.0309	-0.1438	-0.0960	0.1514	0.0140	0.0438	0.0554	0.0366	0.1102	-0.0846	-0.2633	-0.0264	0.0253	0.0396	-0.2838	0.1378	0.1130	0.1033	0.0235	-0.0324	-0.0378	-0.1469	0.1649	-0.0185	0.0227	0.0486	-0.1838	-0.1528	-0.0809	0.1147	-0.1452	-0.1229	0.1140	0.1800	-0.1515	0.1021	-0.2756	0.1124	-0.1177	-0.1865	-0.0846	0.3693	-0.0400	0.0344	-0.0398	-0.0419	-0.1662	-0.0680	-0.1263	-0.2613	0.1181	-0.1330	-0.0210	-0.0101	-0.0367	0.0148	0.0366	0.0270	0.0411
2068e3	2068e3	Eosinophils	d2068	8	#66A61E	2068e3	-0.0540	0.0291	-0.0540	0.0291	-0.1134	0.1366	-0.1202	0.1572	-0.0189	0.0571	-0.1988	-0.0787	0.0511	-0.1154	0.0417	0.0031	-0.1260	-0.1479	-0.0777	-0.1754	0.0278	-0.0937	-0.2378	0.2204	-0.0712	0.1110	0.0011	0.1076	-0.1662	0.2525	-0.0342	-0.4469	0.0539	0.2062	0.1669	-0.0873	-0.1034	0.0247	-0.1366	0.0920	0.2140	0.0321	-0.1551	0.0640	0.0744	-0.0521	0.0622	0.0574	0.1129	0.0443	0.0953	-0.0902	-0.1144	0.0333	-0.0720	0.0502	0.0443	-0.2422	0.0722	0.0090	0.0123	-0.0127	0.0494
2072m3	2072m3	Monocytes	d2072	10	#7570B3	2072m3	0.1625	-0.3357	0.1625	-0.3357	0.2955	-0.0956	-0.2287	0.2039	-0.0977	0.1318	-0.0571	0.3069	0.0459	-0.0693	0.1897	-0.0507	0.1170	-0.0095	-0.1111	-0.1409	-0.0341	0.0536	-0.3146	-0.1473	0.2528	0.0502	0.0895	-0.0005	0.0458	-0.3146	0.1573	-0.0294	-0.0334	-0.0616	0.0182	0.0705	0.0398	0.0094	-0.0377	0.1133	-0.0350	0.0447	0.0010	0.0288	0.1108	-0.0233	0.0170	-0.0861	0.0614	0.0207	-0.1650	-0.0250	-0.1110	0.0516	0.0662	-0.0009	-0.0724	-0.0466	0.0371	0.0288	0.0229	0.0272	0.0028
2072n3	2072n3	Neutrophils	d2072	10	#D95F02	2072n3	-0.0536	0.0794	-0.0536	0.0794	-0.0600	-0.1362	-0.0357	0.0888	-0.1164	-0.0219	-0.0146	0.0624	0.0043	0.0381	-0.0198	-0.1764	0.0345	0.1458	0.0255	0.0548	-0.0337	0.0730	-0.0508	-0.0723	0.1248	0.1205	0.0389	-0.0222	-0.0417	0.3107	-0.0482	0.1221	0.0993	0.0568	0.0051	-0.1119	-0.0115	0.1336	-0.0179	0.3119	0.2813	0.1722	0.4601	-0.2288	-0.2110	-0.1478	0.0190	-0.2426	-0.0967	-0.0250	-0.0509	0.1619	0.0762	0.1120	0.0155	-0.0503	0.0209	-0.0529	-0.0184	0.0108	0.0238	0.0033	-0.0270
2072e3	2072e3	Eosinophils	d2072	10	#66A61E	2072e3	-0.0123	0.0018	-0.0123	0.0018	-0.0979	0.0877	-0.0520	0.0555	-0.1127	-0.0211	-0.2100	-0.0713	-0.0239	-0.2072	0.0803	0.0769	0.1858	-0.1134	0.1081	0.0936	0.1654	-0.0056	0.0763	-0.1180	-0.0910	-0.1330	0.0263	-0.0543	-0.2560	-0.0151	-0.0349	0.0776	0.0205	-0.1483	-0.0368	-0.1735	0.0936	0.0405	-0.0954	-0.0926	-0.0412	-0.0756	0.1707	0.1787	0.0179	0.1165	0.4448	-0.2929	0.0768	0.1504	0.0232	-0.1833	-0.1542	0.0850	-0.0413	-0.0316	0.0798	0.2614	0.0072	-0.0698	-0.0232	-0.0134	-0.0213
2159bp1	2159bp1	Biopsy	d2159	12	#E7298A	2159bp1	-0.0063	0.0209	-0.0063	0.0209	-0.0762	0.0015	-0.0088	0.0519	-0.0734	-0.0845	-0.0898	0.0664	0.0123	0.1132	-0.0198	0.0046	0.0299	0.0747	0.0892	0.0424	-0.0085	0.0147	-0.0181	-0.0195	0.0437	0.0074	0.0635	-0.0124	0.0997	-0.0024	0.0538	0.0440	0.0909	0.0311	0.0930	0.0013	0.0113	-0.0091	0.0352	-0.0790	-0.0222	0.0281	0.0275	-0.0284	0.0465	0.1310	0.0095	0.0993	0.0140	0.1604	-0.0036	-0.0522	0.1469	-0.0075	-0.0644	0.1386	0.0569	0.0091	0.0219	0.0407	0.0420	-0.0310	0.5089
2073m3	2073m3	Monocytes	d2073	11	#7570B3	2073m3	0.0407	-0.2370	0.0407	-0.2370	0.0956	-0.0853	0.0482	-0.0780	0.0423	-0.0192	-0.0095	-0.2838	0.2004	0.1176	-0.0954	-0.0259	0.0425	0.0641	-0.1318	-0.0200	0.0096	-0.0691	0.0837	0.3081	0.2924	0.2636	0.0237	-0.1490	-0.0333	0.2781	-0.0124	0.1186	0.0362	-0.0010	0.0239	-0.0932	-0.2119	-0.1851	0.1770	0.0853	-0.3530	-0.0243	-0.0109	0.1166	0.1805	0.0430	0.0801	-0.1347	0.0057	0.0823	-0.0676	0.0126	-0.0870	0.0104	0.0665	-0.0136	0.0158	0.0232	-0.0312	-0.0238	-0.0089	0.0396	-0.0022
2073n3	2073n3	Neutrophils	d2073	11	#D95F02	2073n3	-0.1386	0.0840	-0.1386	0.0840	0.0111	-0.3333	-0.0818	0.0948	0.1439	-0.0603	0.1411	-0.1514	-0.0296	-0.0134	0.2000	0.4356	-0.0489	-0.0438	-0.0154	-0.0331	0.0351	-0.1335	0.0207	0.1000	0.3650	-0.1485	-0.2026	0.3503	-0.2156	0.0325	0.1292	0.1242	0.0971	0.0266	-0.0083	0.0736	0.1874	0.1220	0.0035	-0.0962	0.0193	0.0714	-0.0091	-0.0674	-0.0260	0.0388	0.0039	0.0429	-0.0426	0.0398	-0.0167	0.0254	0.0224	-0.0360	-0.0164	0.0233	0.0132	-0.0252	0.0337	0.0248	0.0098	0.0048	-0.0220
2073e3	2073e3	Eosinophils	d2073	11	#66A61E	2073e3	-0.0772	-0.0005	-0.0772	-0.0005	-0.1131	0.0964	-0.0729	0.1072	-0.0513	0.0128	-0.1006	0.0166	-0.0016	0.0459	0.0164	0.0031	0.0083	0.0763	0.0435	0.0751	-0.1214	0.0397	-0.1567	0.0186	0.0672	0.0061	-0.0745	0.0114	0.1100	0.1901	0.1018	-0.2604	-0.0376	0.2155	-0.0024	0.1069	0.0352	-0.0887	0.0346	-0.4074	-0.0820	-0.0911	-0.0131	-0.1446	-0.0616	-0.1999	-0.0358	-0.0277	0.0098	-0.0639	-0.2991	0.0206	0.1179	0.0495	0.1530	-0.1233	-0.0246	0.4900	-0.0448	-0.0763	-0.0485	0.0677	-0.1024
2162m1	2162m1	Monocytes	d2162	13	#7570B3	2162m1	-0.0865	-0.1744	-0.0865	-0.1744	0.1030	-0.0725	0.7377	0.4497	0.1370	0.2638	-0.1277	0.0097	-0.1694	-0.0785	-0.1163	-0.0016	-0.0451	0.0241	0.0917	-0.0496	0.0496	-0.0252	0.0079	-0.0071	0.0237	-0.0371	0.0054	-0.0175	0.0254	0.0097	0.0051	-0.0053	-0.0347	-0.0024	0.0027	0.0159	0.0141	0.0169	-0.0187	-0.0154	0.0063	0.0052	0.0021	-0.0101	-0.0096	-0.0005	0.0090	-0.0013	-0.0001	-0.0337	0.0629	0.0141	0.0275	-0.0345	-0.0120	0.0085	0.0213	0.0138	-0.0029	-0.0066	0.0025	-0.0047	-0.0018
2162n1	2162n1	Neutrophils	d2162	13	#D95F02	2162n1	-0.1912	0.0761	-0.1912	0.0761	0.0569	-0.1689	-0.1478	0.0180	0.3067	0.0943	-0.0843	-0.0916	-0.1356	0.1721	0.1209	0.4864	0.0129	-0.0324	-0.0255	-0.0044	-0.1426	0.0024	-0.0561	-0.1762	-0.2634	0.2650	0.1816	-0.3776	0.1075	-0.0001	-0.0109	0.0227	-0.2108	0.0311	0.0219	-0.0145	-0.0206	-0.1232	-0.1060	0.0774	0.0310	0.0133	0.0521	-0.0003	-0.0133	-0.0136	-0.0051	-0.0344	0.0209	0.0045	0.0157	0.0021	0.0054	-0.0099	-0.0031	-0.0057	0.0294	0.0049	0.0083	-0.0061	-0.0106	-0.0028	0.0069
2162e1	2162e1	Eosinophils	d2162	13	#66A61E	2162e1	-0.2873	0.0421	-0.2873	0.0421	0.1790	0.5985	-0.2023	0.2829	-0.0393	0.2347	0.3881	-0.2399	-0.0923	0.1671	0.0117	-0.0187	0.0458	0.1849	-0.0166	-0.0230	0.0212	0.0006	0.0898	0.0188	0.0674	-0.0993	0.0547	-0.0046	0.0046	-0.0602	-0.0088	0.0558	0.0158	-0.0503	0.0615	-0.0096	0.0354	0.0235	0.0237	0.0349	0.0256	0.0045	0.0355	0.0343	0.0172	0.0159	-0.0168	-0.0191	-0.0169	0.0175	0.0193	0.0059	-0.0087	0.0043	-0.0020	0.0090	0.0021	-0.0218	-0.0093	0.0158	0.0084	-0.0061	0.0034
2162bp1	2162bp1	Biopsy	d2162	13	#E7298A	2162bp1	0.0015	0.0479	0.0015	0.0479	-0.0517	0.0133	-0.0088	0.0765	-0.0684	-0.1155	-0.0933	0.0818	0.0368	0.1439	-0.0432	0.0146	-0.0160	0.0209	0.0640	0.0313	0.0534	0.0342	-0.0627	-0.0248	0.0055	0.0038	0.1210	0.0173	0.1513	-0.0217	0.0176	0.0238	0.0901	0.0054	0.1430	-0.0355	-0.0474	-0.0250	0.1311	-0.0576	-0.0224	0.0391	0.0519	-0.0696	0.0649	0.2580	0.0732	0.1380	0.1153	0.2761	0.0558	-0.0454	0.2500	-0.0673	-0.0658	0.1745	0.0402	-0.0491	0.1433	0.1992	0.1780	0.0068	-0.6415
macrofagos	Macrofagos	macrophage	unknown	14	#E6AB02	Macrofagos	0.1075	0.0624	0.1075	0.0624	-0.0026	0.0136	0.0068	-0.0267	-0.0182	-0.0565	-0.0157	0.0460	-0.1562	0.0452	-0.0102	0.0170	-0.0393	0.0172	0.0535	-0.0129	0.0036	-0.0537	0.0727	0.0564	0.1401	0.0445	-0.1521	-0.0676	0.0486	-0.1644	-0.1324	-0.1287	-0.0779	0.0376	0.1734	-0.2674	0.1577	-0.1194	0.1756	0.1029	0.0224	-0.1022	-0.0765	-0.0020	-0.1265	0.1066	0.0035	0.0033	0.0948	-0.0611	-0.0801	0.3239	-0.1458	0.0275	-0.4889	-0.3210	-0.1308	0.1311	0.1721	0.1270	0.0476	0.0045	0.0410
macrofagos+sbv	Macrofagos+SbV	macrophage	unknown	14	#E6AB02	Mcrfgs+SbV	0.2461	0.2008	0.2461	0.2008	0.1284	0.0689	0.0658	-0.0190	0.1453	0.0041	0.0322	-0.0069	0.1318	0.1484	0.0892	-0.0168	-0.0711	-0.0070	0.1284	0.0339	0.1182	-0.0054	-0.1291	0.0941	0.0056	-0.0390	-0.1253	-0.0184	0.0758	0.0320	-0.0235	-0.1005	-0.1182	-0.0772	-0.2271	-0.1288	0.2476	-0.0879	0.0001	0.1336	-0.0659	0.0417	-0.0707	0.1226	-0.2301	-0.1075	-0.0328	-0.0404	-0.0050	-0.0290	-0.0372	-0.1122	-0.0262	0.1829	0.0457	0.3001	0.1198	0.0454	-0.1550	-0.0327	0.4729	0.1243	0.0135
macrofagos+10772	Macrofagos+10772	macrophage	unknown	14	#E6AB02	Mcrf+10772	0.2056	0.1108	0.2056	0.1108	0.1114	0.0386	-0.0039	-0.0446	-0.0178	-0.0793	0.0133	-0.0774	-0.4173	-0.0848	-0.0089	-0.0801	-0.0121	-0.1084	-0.2017	0.1012	0.0244	-0.0448	-0.0754	0.0394	0.0799	0.0152	0.0092	-0.1854	0.0835	0.1190	0.1686	0.0233	0.1395	0.0716	-0.1372	0.0929	0.0208	0.1435	-0.1329	-0.0665	0.0010	-0.0209	0.1643	0.2207	0.0675	0.2152	-0.0488	0.3140	-0.0222	-0.0452	0.1309	0.1730	-0.0631	0.3078	0.1636	-0.1111	0.1397	0.0343	0.0826	0.0194	-0.0228	0.0999	-0.0173
macrofagos+10772+sbv	Macrofagos+10772+SbV	macrophage	unknown	14	#E6AB02	M+10772+SV	0.2185	0.2072	0.2185	0.2072	0.0968	0.0655	0.0649	0.0064	0.0686	0.0420	-0.0106	0.0185	0.1521	0.0727	0.0926	0.0297	0.0525	0.0316	0.0874	0.0657	0.0392	0.0298	-0.1354	0.0649	0.0206	-0.0418	-0.1093	-0.0217	0.1580	0.0680	0.0033	-0.0423	-0.0111	-0.0349	-0.0842	-0.0708	0.1283	-0.0239	0.0527	0.0959	0.0400	-0.0103	0.0440	0.0691	-0.0601	0.0496	0.0164	0.0632	0.0006	0.1048	-0.0172	-0.0201	-0.0325	-0.1031	-0.0250	0.1805	-0.1038	-0.0367	-0.0905	-0.0068	-0.7734	-0.0599	-0.0639
macrofagos+2169	Macrofagos+2169	macrophage	unknown	14	#E6AB02	Mcrfg+2169	0.2075	0.1163	0.2075	0.1163	0.1052	0.0516	-0.0051	-0.0546	-0.0783	0.0077	-0.0131	-0.0856	-0.4097	-0.2387	-0.0120	0.0967	0.2515	-0.0537	-0.1953	-0.0115	-0.1604	-0.0282	-0.0253	0.0483	-0.1415	-0.1178	-0.1484	0.0902	0.1894	0.1078	0.0539	0.0158	0.1682	-0.0668	-0.0124	-0.0026	-0.0740	-0.1361	0.1849	0.1350	-0.0900	0.0784	-0.0782	-0.1228	-0.0034	-0.1468	-0.0507	-0.2562	0.1024	-0.0052	-0.0253	-0.2210	0.2015	-0.2459	-0.0358	-0.0223	-0.0029	-0.0736	0.0487	-0.0050	0.0737	-0.0478	0.0350
macrofagos+2169+sbv	Macrofagos+2169+SbV	macrophage	unknown	14	#E6AB02	Mc+2169+SV	0.1373	0.1042	0.1373	0.1042	-0.0025	0.0808	0.0537	-0.0552	-0.0173	0.1008	-0.0798	-0.0615	0.1800	-0.1861	0.0171	0.2126	0.1882	0.0261	0.1041	-0.0116	-0.1441	-0.0372	0.0863	-0.0288	-0.0214	-0.1475	0.0050	0.0450	-0.0065	-0.1902	-0.0367	-0.0772	0.0127	-0.0266	0.2919	-0.0125	-0.4631	0.1180	0.0466	0.0435	-0.1496	0.3111	0.0885	-0.0204	-0.1693	-0.0448	-0.0532	0.2274	-0.1584	-0.0403	-0.0609	0.1352	-0.1521	0.1400	0.0222	0.0554	0.1130	0.0867	-0.1078	-0.0144	0.0197	0.0631	-0.0260
macrofagos+12309	Macrofagos+12309	macrophage	unknown	14	#E6AB02	Mcrf+12309	0.1760	0.0807	0.1760	0.0807	0.0805	0.0380	0.0045	-0.0505	0.0507	-0.1267	0.0124	-0.0273	-0.2743	0.0785	-0.0038	-0.0654	-0.2135	-0.0818	-0.0249	0.0154	0.1121	-0.0533	0.0376	-0.0535	0.2242	0.0647	0.1305	-0.0749	-0.1032	-0.1056	-0.1680	-0.0202	-0.0622	0.0842	0.0420	0.0436	-0.1979	0.1089	-0.0474	-0.1188	0.0487	-0.0785	0.0353	-0.0680	-0.0390	-0.1273	0.0613	0.0065	-0.0843	0.0640	-0.1260	-0.0489	-0.1160	-0.1806	0.0139	0.1844	-0.1184	0.0403	-0.1721	-0.1024	0.0795	-0.5829	-0.0336
macrofagos+12309+sbv	Macrofagos+12309+SbV	macrophage	unknown	14	#E6AB02	M+12309+SV	0.2401	0.2395	0.2401	0.2395	0.1023	0.0786	0.1011	-0.0291	0.1936	0.0718	0.0478	0.0124	0.3254	0.0345	0.0863	0.0073	-0.0142	0.0210	-0.0070	-0.0557	0.0624	0.0106	0.0704	-0.0359	-0.0557	-0.0274	-0.0331	-0.2144	-0.0567	0.0132	0.1386	-0.0281	0.3345	-0.0719	-0.0158	0.2111	-0.0649	0.0514	-0.1504	-0.1201	0.1505	-0.1438	0.0968	-0.1818	0.2465	-0.0503	0.0849	-0.0401	0.0656	0.0468	-0.0183	0.1058	-0.0597	-0.2660	-0.0841	-0.2292	-0.1312	-0.0364	-0.0264	-0.0088	0.1811	0.1571	0.0327
macrofagos+12367+sbv	Macrofagos+12367+SbV	macrophage	unknown	14	#E6AB02	M+12367+SV	0.1979	0.1639	0.1979	0.1639	0.0752	0.0542	0.0522	-0.0151	0.1168	0.0107	0.0379	0.0100	0.1519	0.0780	0.0017	-0.0240	-0.1011	0.0208	0.0714	-0.0443	-0.0055	0.0105	-0.0416	-0.0013	-0.0231	0.0282	0.1041	0.0789	-0.1436	-0.0849	-0.0141	-0.0025	-0.0892	-0.0852	0.0130	-0.0736	-0.0020	-0.0530	0.0193	-0.0916	-0.0508	0.1452	-0.1618	-0.1218	0.0349	0.0311	-0.0080	-0.1995	-0.1361	-0.0418	0.1378	-0.0705	0.2433	0.2726	0.2497	-0.3390	0.1414	-0.0361	0.4261	0.0214	-0.0927	-0.2968	0.0381
macrofagos+1126	Macrofagos+1126	macrophage	unknown	14	#E6AB02	Mcrfg+1126	0.1270	0.0400	0.1270	0.0400	0.0326	0.0177	-0.0116	-0.0324	0.0143	-0.1415	0.0026	-0.0063	-0.2474	0.0988	-0.0608	-0.0595	-0.1772	-0.0482	0.0449	-0.0309	0.0797	-0.0606	0.0482	-0.0660	0.1270	0.0320	0.0863	0.0100	-0.1811	-0.1583	-0.1977	0.0010	-0.1754	0.0134	0.1263	-0.0630	-0.1217	0.0097	0.0304	-0.1155	0.0658	-0.0012	-0.0339	-0.0973	-0.0189	-0.0786	0.0153	-0.1216	-0.0564	0.0476	0.0306	-0.1342	0.0826	-0.1035	0.1616	0.0237	-0.0307	-0.0878	-0.0306	0.0237	-0.1548	0.6851	0.0425
macrofagos+12251	Macrofagos+12251	macrophage	unknown	14	#E6AB02	Mcrf+12251	0.0834	0.1119	0.0834	0.1119	-0.0464	-0.0147	0.0026	0.0197	-0.0440	0.0486	0.0788	0.1097	-0.0598	-0.1309	-0.0925	-0.1068	0.0638	0.1169	-0.1527	-0.1035	-0.2245	-0.0013	0.1096	-0.0471	-0.0943	0.1316	-0.0524	-0.0559	-0.2128	0.0684	0.1320	0.1350	-0.0767	0.0379	0.1141	0.0782	0.1815	-0.1440	-0.0756	-0.0946	0.0333	0.0732	-0.3286	-0.2589	0.1374	0.1551	0.0363	-0.1235	-0.1882	0.1200	0.0789	0.1449	-0.0910	0.2637	-0.1461	0.2775	-0.0462	0.0268	-0.2446	-0.0669	-0.0323	0.0076	-0.0854
macrofagos+12251+sbv	Macrofagos+12251+SbV	macrophage	unknown	14	#E6AB02	M+12251+SV	0.1751	0.1842	0.1751	0.1842	0.0530	0.0392	0.0464	0.0145	-0.0390	0.0937	0.0068	0.0173	0.0806	-0.0511	0.0195	-0.0019	0.0911	0.0851	0.0532	-0.0075	-0.2133	0.1305	-0.0585	-0.1372	-0.0482	0.1926	0.1577	0.3905	-0.0733	0.2072	-0.1329	0.3526	-0.2949	0.1751	0.0013	0.0481	-0.0243	0.1384	0.0747	-0.0782	0.0376	-0.1746	0.0184	0.2669	0.0968	0.0126	-0.0958	0.0993	0.2197	-0.0799	-0.0319	-0.0563	-0.0910	-0.0937	-0.0833	-0.0862	-0.0036	0.0051	0.0154	0.0039	0.0890	0.0224	0.0056

write.csv(all_pca$table, file="hs_donor_pca_coords.csv")
plot_corheat(all_norm)$plot

plot_topn(hs_valid)$plot

## `geom_smooth()` using formula 'y ~ x'

5 Cell types

The following blocks split the samples into a few groups by sample type and look at the distributions between them.

5.1 Monocytes

mono <- subset_expt(hs_valid, subset="typeofcells=='Monocytes'")

## Using a subset expression.

## There were 63, now there are 11 samples.

mono <- set_expt_conditions(mono, fact="visitnumber")
mono <- set_expt_batches(mono, fact="donor")
mono_norm <- sm(normalize_expt(mono, transform="log2", convert="cpm", batch="svaseq", filter=TRUE))
plot_pca(mono_norm)$plot

5.2 Neutrophils

neut <- subset_expt(hs_valid, subset="typeofcells=='Neutrophils'")

## Using a subset expression.

## There were 63, now there are 12 samples.

neut <- set_expt_conditions(neut, fact="visitnumber")
neut <- set_expt_batches(neut, fact="donor")
neut_norm <- sm(normalize_expt(neut, transform="log2", convert="cpm", batch="svaseq", filter=TRUE))
plot_pca(neut_norm)$plot

5.3 Eosinophils

eo <- subset_expt(hs_valid, subset="typeofcells=='Eosinophils'")

## Using a subset expression.

## There were 63, now there are 11 samples.

eo <- set_expt_conditions(eo, fact="visitnumber")
eo <- set_expt_batches(eo, fact="donor")
eo_norm <- sm(normalize_expt(eo, transform="log2", convert="cpm", batch="svaseq", filter=TRUE))
plot_pca(eo_norm)$plot

5.4 Question 1

I interpreted question 1 as: pull out tmrc3000[1-6] and look at them.

I am not entirely certain what is meant by the heirarchical clustering request. I can see a couple of possibilities for what this means. The most similar thing I recall in the cruzi context was a post-DE visualization of some fairly specific genes.

hs_q1 <- subset_expt(hs_valid, subset="donor=='d1010'|donor=='d1011'")

## Using a subset expression.

## There were 63, now there are 6 samples.

q1_norm <- sm(normalize_expt(hs_q1, norm="quant", transform="log2", convert="cpm", batch=FALSE,
                           filter=TRUE))
q1_pca <- plot_pca(q1_norm)
q1_pca$plot

knitr::kable(q1_pca$table)

	sampleid	condition	batch	batch_int	colors	labels	PC1	PC2	pc_1	pc_2	pc_3	pc_4	pc_5
1010-2	1010-2	PBMCs	d1010	1	#1B9E77	1010-2	-0.5759	0.2704	-0.5759	0.2704	0.4004	-0.0566	0.5148
1010-7	1010-7	PBMCs	d1010	1	#1B9E77	1010-7	0.0048	0.4828	0.0048	0.4828	-0.6648	0.3977	-0.0112
1010-12	1010-12	PBMCs	d1010	1	#1B9E77	1010-12	0.4107	0.4514	0.4107	0.4514	0.4033	-0.3107	-0.4492
1011-2	1011-2	PBMCs	d1011	2	#1B9E77	1011-2	-0.4764	-0.4166	-0.4764	-0.4166	-0.2714	-0.3745	-0.4679
1011-7	1011-7	PBMCs	d1011	2	#1B9E77	1011-7	0.1313	-0.4486	0.1313	-0.4486	0.3425	0.6930	-0.1315
1011-12	1011-12	PBMCs	d1011	2	#1B9E77	1011-12	0.5054	-0.3394	0.5054	-0.3394	-0.2100	-0.3488	0.5449

write.csv(q1_pca$table, file="q1_pca_coords.csv")

## Looks like PC1 == Time and PC2 is donor, and they have pretty much the same amount of variance

hs_time <- set_expt_conditions(hs_q1, fact="time")
time_norm <- sm(normalize_expt(hs_time, transform="log2",
                               batch="svaseq", filter=TRUE))
## Get a set of genes with high PC loads for PC1(time), and PC2(donor):
high_scores <- pca_highscores(time_norm, n=40)

time_stuff <- high_scores$highest[, c(1, 2)]
time_stuff

##       Comp.1                  Comp.2                 
##  [1,] "16.16:ENSG00000090382" "25.38:ENSG00000197746"
##  [2,] "13.73:ENSG00000075624" "25.27:ENSG00000198804"
##  [3,] "11.74:ENSG00000134954" "23.59:ENSG00000090382"
##  [4,] "9.364:ENSG00000100201" "23.19:ENSG00000075624"
##  [5,] "8.07:ENSG00000038427"  "20.06:ENSG00000038427"
##  [6,] "7.57:ENSG00000168685"  "18.63:ENSG00000019582"
##  [7,] "7.411:ENSG00000125538" "16.41:ENSG00000128016"
##  [8,] "7.029:ENSG00000121966" "14.33:ENSG00000124942"
##  [9,] "6.882:ENSG00000111913" "14.09:ENSG00000163131"
## [10,] "6.372:ENSG00000196924" "12.33:ENSG00000265972"
## [11,] "6.157:ENSG00000100345" "11.94:ENSG00000085265"
## [12,] "5.808:ENSG00000118515" "11.62:ENSG00000163220"
## [13,] "5.627:ENSG00000136167" "11.33:ENSG00000196924"
## [14,] "5.529:ENSG00000197629" "11.19:ENSG00000130066"
## [15,] "5.43:ENSG00000165168"  "10.93:ENSG00000121966"
## [16,] "5.202:ENSG00000159388" "10.88:ENSG00000136167"
## [17,] "5.022:ENSG00000081237" "9.705:ENSG00000210082"
## [18,] "4.791:ENSG00000128016" "9.435:ENSG00000159388"
## [19,] "4.743:ENSG00000171223" "9.296:ENSG00000125538"
## [20,] "4.726:ENSG00000152518" "8.735:ENSG00000116741"
## [21,] "4.623:ENSG00000188404" "8.497:ENSG00000211459"
## [22,] "4.572:ENSG00000081059" "8.324:ENSG00000245532"
## [23,] "4.409:ENSG00000110324" "8.174:ENSG00000165168"
## [24,] "4.405:ENSG00000122566" "8.052:ENSG00000087086"
## [25,] "4.316:ENSG00000127951" "7.82:ENSG00000081237" 
## [26,] "4.268:ENSG00000140575" "7.648:ENSG00000118515"
## [27,] "4.13:ENSG00000245532"  "7.608:ENSG00000211592"
## [28,] "4.045:ENSG00000101347" "7.603:ENSG00000197629"
## [29,] "3.878:ENSG00000109971" "6.782:ENSG00000160255"
## [30,] "3.842:ENSG00000196405" "6.652:ENSG00000184009"
## [31,] "3.793:ENSG00000185811" "6.466:ENSG00000100345"
## [32,] "3.756:ENSG00000120129" "6.402:ENSG00000171223"
## [33,] "3.677:ENSG00000130066" "6.349:ENSG00000119535"
## [34,] "3.557:ENSG00000082074" "6.297:ENSG00000137076"
## [35,] "3.544:ENSG00000073756" "6.165:ENSG00000185215"
## [36,] "3.468:ENSG00000116741" "6.085:ENSG00000152518"
## [37,] "3.441:ENSG00000184009" "6.079:ENSG00000140575"
## [38,] "3.091:ENSG00000197043" "5.692:ENSG00000135821"
## [39,] "3.049:ENSG00000160593" "5.496:ENSG00000123384"
## [40,] "3.019:ENSG00000182578" "5.28:ENSG00000000938"

## Column 1 should be winners vs. time and column 2 by donor.
time_genes <- gsub(x=time_stuff[, "Comp.1"], pattern="^.*:(.*)$", replacement="\\1")
head(time_genes)

## [1] "ENSG00000090382" "ENSG00000075624" "ENSG00000134954" "ENSG00000100201"
## [5] "ENSG00000038427" "ENSG00000168685"

time_subset <- exprs(time_norm)[time_genes, ]
plot_sample_heatmap(time_norm, row_label=rownames(time_norm))

hs_donor <- set_expt_conditions(hs_q1, fact="donor")
donor_norm <- sm(normalize_expt(hs_donor, convert="cpm", transform="log2",
                                batch="svaseq", filter=TRUE))
## Get a set of genes with high PC loads for PC1(donor), and PC2(donor):
high_scores <- pca_highscores(donor_norm, n=40)

donor_stuff <- high_scores$highest[, c(1, 2)]
donor_stuff

##       Comp.1                  Comp.2                 
##  [1,] "117.6:ENSG00000090382" "11.46:ENSG00000118503"
##  [2,] "66.31:ENSG00000198804" "8.971:ENSG00000100316"
##  [3,] "42.52:ENSG00000198938" "8.813:ENSG00000167658"
##  [4,] "37.86:ENSG00000198886" "8.072:ENSG00000149273"
##  [5,] "31.64:ENSG00000198899" "8.008:ENSG00000156508"
##  [6,] "31.55:ENSG00000198763" "7.546:ENSG00000142541"
##  [7,] "29.58:ENSG00000163220" "7.511:ENSG00000112306"
##  [8,] "28.16:ENSG00000121966" "7.388:ENSG00000121966"
##  [9,] "28.09:ENSG00000198888" "7.346:ENSG00000164587"
## [10,] "27.93:ENSG00000265972" "6.672:ENSG00000198034"
## [11,] "21.72:ENSG00000118503" "6.443:ENSG00000167526"
## [12,] "17.95:ENSG00000157514" "5.733:ENSG00000107742"
## [13,] "16.67:ENSG00000143384" "5.468:ENSG00000108298"
## [14,] "16.35:ENSG00000038427" "5.435:ENSG00000174444"
## [15,] "14.46:ENSG00000129824" "5.197:ENSG00000171223"
## [16,] "13.78:ENSG00000067048" "5.165:ENSG00000063177"
## [17,] "13.29:ENSG00000152518" "5.052:ENSG00000137154"
## [18,] "12.95:ENSG00000237973" "5.001:ENSG00000167978"
## [19,] "12.19:ENSG00000026025" "4.994:ENSG00000142937"
## [20,] "11.7:ENSG00000225630"  "4.971:ENSG00000142676"
## [21,] "11.69:ENSG00000198712" "4.962:ENSG00000177600"
## [22,] "11.32:ENSG00000135046" "4.855:ENSG00000128016"
## [23,] "11.09:ENSG00000119535" "4.747:ENSG00000105372"
## [24,] "9.689:ENSG00000124942" "4.715:ENSG00000197756"
## [25,] "9.384:ENSG00000012817" "4.439:ENSG00000076928"
## [26,] "9.14:ENSG00000163131"  "4.438:ENSG00000156482"
## [27,] "8.384:ENSG00000087086" "4.317:ENSG00000178209"
## [28,] "7.99:ENSG00000128016"  "4.273:ENSG00000163346"
## [29,] "7.854:ENSG00000133112" "4.147:ENSG00000161016"
## [30,] "7.483:ENSG00000139318" "4.093:ENSG00000205542"
## [31,] "7.341:ENSG00000173821" "4.002:ENSG00000157514"
## [32,] "6.924:ENSG00000137154" "3.971:ENSG00000105193"
## [33,] "6.645:ENSG00000118515" "3.958:ENSG00000144713"
## [34,] "6.463:ENSG00000197629" "3.933:ENSG00000145592"
## [35,] "6.244:ENSG00000142102" "3.822:ENSG00000180448"
## [36,] "6.071:ENSG00000136167" "3.798:ENSG00000213741"
## [37,] "6.032:ENSG00000170345" "3.768:ENSG00000179094"
## [38,] "5.936:ENSG00000170776" "3.675:ENSG00000008988"
## [39,] "5.851:ENSG00000179344" "3.625:ENSG00000137818"
## [40,] "5.791:ENSG00000120129" "3.604:ENSG00000071082"

## Column 1 should be winners vs. donor and column 2 by donor.
donor_genes <- gsub(x=donor_stuff[, "Comp.1"], pattern="^.*:(.*)$", replacement="\\1")
head(donor_genes)

## [1] "ENSG00000090382" "ENSG00000198804" "ENSG00000198938" "ENSG00000198886"
## [5] "ENSG00000198899" "ENSG00000198763"

donor_subset <- exprs(donor_norm)[donor_genes, ]
plot_sample_heatmap(donor_norm, row_label=rownames(donor_norm))

time_keepers <- list(
  "2hr_vs_7hr" = c("t2hr", "t7hr"),
  "2hr_vs_12hr" = c("t2hr", "t12hr"),
  "7hr_vs_12hr" = c("t7hr", "t12hr"))

q1_time <- set_expt_conditions(hs_q1, fact="time")
time_de <- sm(all_pairwise(q1_time, model_batch=FALSE, parallel=FALSE))

time_all_tables <- sm(combine_de_tables(time_de,
                                        excel=glue::glue("excel/time_de_tables-v{ver}.xlsx")))

time_all_tables_all <- sm(combine_de_tables(
  time_de,
  keepers="all",
  excel=glue::glue("excel/time_de_all_tables-v{ver}.xlsx")))

time_all_tables <- sm(combine_de_tables(
  time_de,
  keepers=time_keepers,
  excel=glue::glue("excel/{rundate}-time_de_tables-v{ver}.xlsx")))

q1_donor <- set_expt_conditions(hs_q1, fact="donor")
donor_de <- sm(all_pairwise(q1_donor, model_batch=FALSE))
donor_tables <- sm(combine_de_tables(
  donor_de, excel=glue::glue("excel/donor_de_tables-v{ver}.xlsx")))

hs_q2 <- subset_expt(hs_valid, subset="donor!='d1010'&donor!='d1011'")

## Using a subset expression.

## There were 63, now there are 56 samples.

q2_norm <- sm(normalize_expt(hs_q2, transform="log2", convert="cpm", norm="quant", filter=TRUE))

q2_pca <- plot_pca(q2_norm)
knitr::kable(q2_pca$table)

	sampleid	condition	batch	batch_int	colors	labels	PC1	PC2	pc_1	pc_2	pc_3	pc_4	pc_5	pc_6	pc_7	pc_8	pc_9	pc_10	pc_11	pc_12	pc_13	pc_14	pc_15	pc_16	pc_17	pc_18	pc_19	pc_20	pc_21	pc_22	pc_23	pc_24	pc_25	pc_26	pc_27	pc_28	pc_29	pc_30	pc_31	pc_32	pc_33	pc_34	pc_35	pc_36	pc_37	pc_38	pc_39	pc_40	pc_41	pc_42	pc_43	pc_44	pc_45	pc_46	pc_47	pc_48	pc_49	pc_50	pc_51	pc_52	pc_53	pc_54
1034n1	1034n1	Neutrophils	d1034	1	#D95F02	1034n1	-0.1948	-0.0374	-0.1948	-0.0374	-0.1797	-0.0022	-0.0923	0.0805	-0.3242	0.1119	-0.0121	-0.0047	0.0029	-0.1226	0.3067	-0.0960	0.0230	-0.0225	0.1560	-0.0128	0.0599	-0.0553	0.1779	-0.1145	0.4150	-0.0558	-0.0230	-0.0455	-0.0501	-0.1480	-0.4143	0.3231	-0.2237	-0.0448	-0.0370	-0.0307	-0.1689	-0.0764	0.0041	0.0716	0.0441	0.0184	0.0518	0.0261	-0.0600	-0.0095	-0.0075	-0.0254	-0.0006	-0.0008	-0.0018	-0.0078	-0.0077	-0.0013	-0.0020	-0.0039
1034n2	1034n2	Neutrophils	d1034	1	#D95F02	1034n2	-0.1973	-0.0392	-0.1973	-0.0392	-0.2084	0.0052	-0.0925	0.0306	-0.3471	0.2037	0.0195	-0.0418	0.0628	-0.1344	0.3088	-0.1834	-0.1003	0.0916	0.1862	0.1386	0.1569	-0.1155	-0.1732	-0.0763	-0.1382	-0.1440	0.0510	0.0703	-0.0045	0.0960	0.2358	-0.4653	0.1856	0.2165	0.0246	0.0118	0.0810	-0.0113	-0.0173	-0.0681	-0.0175	-0.0360	0.0180	0.0458	0.0190	0.0128	0.0129	0.0144	0.0094	-0.0053	-0.0027	0.0009	0.0041	-0.0053	0.0005	-0.0010
1034m2	1034m2	Monocytes	d1034	1	#7570B3	1034m2	-0.0069	-0.0449	-0.0069	-0.0449	0.0256	-0.2526	0.0782	0.2256	-0.3239	-0.0592	-0.0544	-0.0760	0.0144	-0.0083	0.0333	0.1253	0.2885	-0.1544	-0.2072	-0.0269	0.0085	-0.0016	-0.0045	0.1023	-0.1368	0.1685	-0.0150	-0.0030	-0.0199	-0.0799	0.1504	0.0909	0.0489	-0.0330	-0.0051	-0.0249	-0.0080	-0.0298	0.0575	0.0208	0.0403	0.0286	0.0158	0.0499	0.0451	-0.2081	0.6176	0.1105	-0.1265	0.0819	-0.0465	0.0118	-0.0066	0.0049	0.0013	0.0071
1034m2-	1034m2-	Monocytes	d1034	1	#7570B3	1034m2-	-0.0127	-0.0454	-0.0127	-0.0454	0.0331	-0.2448	0.0703	0.2241	-0.3291	-0.0843	-0.0358	-0.0987	0.0170	0.0638	0.0485	0.0769	0.2508	-0.1399	-0.2494	-0.0390	0.0407	0.0371	0.0203	0.0472	-0.1661	0.0971	0.0151	0.0477	-0.0482	-0.0117	0.0843	0.0619	0.0130	-0.0390	-0.0151	-0.0029	0.0121	0.1019	-0.0062	0.0547	-0.0305	-0.0496	-0.0567	-0.0369	0.0044	0.1667	-0.6574	-0.0790	0.1102	-0.1173	0.0630	0.0014	-0.0063	0.0019	-0.0134	-0.0074
2050bp1	2050bp1	Biopsy	d2050	2	#E7298A	2050bp1	0.1436	-0.1823	0.1436	-0.1823	-0.0106	0.0779	0.0234	-0.0898	-0.0107	0.2247	-0.1399	-0.1446	-0.3779	0.2371	-0.1070	-0.0641	0.2568	0.3061	0.0778	-0.1360	0.2687	-0.0411	-0.1109	-0.1784	-0.0280	0.2719	-0.1833	0.0182	0.1103	-0.0440	-0.0734	-0.0387	-0.1044	0.0768	-0.0829	0.3712	0.0251	0.0259	0.0007	-0.0046	0.0375	0.0577	0.0161	-0.0080	-0.0200	0.0675	0.0266	-0.0075	0.0054	0.0063	0.0154	-0.0131	-0.0434	-0.0113	0.0016	0.0035
2052bp1	2052bp1	Biopsy	d2052	3	#E7298A	2052bp1	0.1498	-0.2043	0.1498	-0.2043	-0.0197	0.1211	0.0385	-0.2114	-0.1280	-0.1195	0.1132	0.1084	0.2633	0.0091	-0.0747	0.1189	0.0516	-0.0081	0.0710	0.1136	-0.0821	0.0397	-0.1109	-0.3298	0.0502	0.2409	-0.1254	0.3185	0.2775	-0.2027	0.0532	-0.0935	-0.2205	0.0164	0.2406	-0.3620	-0.0130	0.0837	0.0153	0.0606	-0.0475	-0.0193	0.0201	0.0149	0.0426	-0.0056	-0.0070	-0.0083	0.0062	-0.0200	-0.0036	-0.0133	0.0010	0.0044	0.0101	0.0026
2052e1	2052e1	Eosinophils	d2052	3	#66A61E	2052e1	-0.0620	0.1427	-0.0620	0.1427	0.1961	0.2141	0.1475	0.0438	0.0548	0.0027	-0.1374	0.1200	0.0207	-0.3013	0.0427	0.1654	0.1217	0.2760	-0.1657	0.0923	0.0703	-0.1726	-0.1578	-0.2062	0.3273	0.1532	0.3493	-0.0953	-0.0993	0.1403	0.3180	0.1633	-0.0226	0.0251	-0.0545	-0.0111	0.0954	-0.0160	-0.0551	0.0810	0.0467	-0.0420	-0.0698	0.0305	-0.0200	0.0328	-0.0471	0.0347	-0.0421	0.0656	-0.0078	0.0198	0.0075	-0.0163	-0.0208	-0.0088
2052n2	2052n2	Neutrophils	d2052	3	#D95F02	2052n2	-0.1189	0.1304	-0.1189	0.1304	-0.1903	0.1989	0.2495	0.1197	0.1226	-0.1527	0.4076	-0.3661	-0.0490	-0.0389	-0.0292	0.2480	0.0436	0.2024	-0.0852	0.3848	0.2677	0.2119	0.2076	0.0711	-0.0239	-0.0240	-0.0714	0.0134	-0.0101	-0.0472	-0.0956	-0.0766	0.0152	0.0173	-0.0076	-0.0123	-0.0351	-0.0429	0.0071	-0.0328	0.0262	0.0073	0.0149	-0.0059	0.0033	-0.0331	0.0047	-0.0100	0.0037	-0.0029	-0.0010	0.0072	0.0001	0.0045	0.0012	0.0026
2065bp1	2065bp1	Biopsy	d2065	4	#E7298A	2065bp1	0.1514	-0.1988	0.1514	-0.1988	-0.0400	0.1034	0.0496	-0.3368	-0.1933	-0.1744	0.1977	0.1528	0.2506	0.0365	-0.0633	0.1234	-0.0411	0.1303	0.0257	-0.3490	0.3323	-0.1651	0.1435	0.3322	0.0394	-0.1218	0.1454	0.1641	-0.0326	0.0425	0.0118	0.1265	0.2174	0.0288	-0.1446	0.0989	-0.0525	0.0224	-0.0090	0.0184	0.0038	-0.0239	-0.0218	0.0044	-0.0046	0.0170	0.0173	0.0188	0.0045	0.0051	-0.0013	0.0010	-0.0066	-0.0101	0.0000	-0.0027
2066bp1	2066bp1	Biopsy	d2066	5	#E7298A	2066bp1	0.1493	-0.2051	0.1493	-0.2051	-0.0359	0.1136	0.0289	-0.0834	-0.0738	-0.0874	0.1066	0.1344	0.2449	-0.0781	0.0202	0.0961	-0.0186	-0.1430	-0.0267	0.0849	-0.0677	0.1030	-0.1121	-0.2001	-0.0954	0.0827	-0.1333	-0.5965	-0.2425	0.1442	-0.1188	-0.1615	-0.0523	-0.0581	-0.1710	0.1950	-0.1769	0.2417	0.0018	-0.0582	0.0072	0.0294	-0.0092	-0.0371	-0.0281	0.0231	0.0263	-0.0042	0.0026	0.0212	-0.0150	-0.0040	0.0044	0.0010	-0.0077	-0.0001
2068m1	2068m1	Monocytes	d2068	6	#7570B3	2068m1	-0.0042	-0.0647	-0.0042	-0.0647	0.0647	-0.2726	0.1514	-0.1798	0.2112	0.1115	0.1400	-0.0402	0.0195	-0.0993	0.2098	-0.1189	-0.0690	0.1227	-0.0179	-0.0130	-0.0840	-0.2294	0.1932	-0.0516	0.0174	0.2151	-0.2108	-0.0089	-0.1616	-0.0398	0.2244	-0.0213	0.1627	-0.3315	0.1643	0.0437	-0.2699	-0.2489	0.2574	-0.0461	-0.0764	-0.0090	0.1320	-0.0324	0.0632	0.0839	-0.0539	-0.0166	-0.0049	0.0130	-0.0085	-0.0198	-0.0137	-0.0062	-0.0004	0.0099
2068n1	2068n1	Neutrophils	d2068	6	#D95F02	2068n1	-0.1901	-0.0495	-0.1901	-0.0495	-0.1401	-0.0170	-0.0614	-0.1513	0.2087	0.0158	-0.0665	0.1093	-0.0279	0.0056	0.0197	-0.0218	0.1989	-0.1787	-0.2026	-0.0099	0.0384	-0.0778	0.2251	-0.0782	0.2110	-0.1650	-0.1821	-0.1372	0.1063	-0.2672	0.1407	-0.0279	0.1290	0.2491	-0.0830	-0.0150	0.1992	0.1372	0.0779	-0.0764	-0.1574	-0.0520	-0.2211	-0.4125	0.1549	-0.0248	0.0257	-0.0416	-0.0296	-0.0103	0.0199	0.0016	-0.0066	0.0059	-0.0025	-0.0067
2068e1	2068e1	Eosinophils	d2068	6	#66A61E	2068e1	-0.1241	-0.0397	-0.1241	-0.0397	0.2479	0.0236	-0.1400	-0.0725	0.1169	-0.0132	0.1474	-0.0501	-0.0290	0.0435	0.0853	-0.1044	0.0497	-0.1966	-0.0261	0.0753	0.1008	-0.2663	0.1749	-0.0389	-0.1357	-0.0026	0.0489	-0.0586	0.2276	-0.0313	0.0424	-0.1384	-0.1088	-0.2400	-0.1822	-0.0279	-0.0436	-0.0739	-0.4396	0.2196	0.0337	0.1907	-0.2653	0.1810	-0.0747	-0.0509	0.0374	-0.0527	0.1841	0.1181	0.0831	0.0129	0.0192	0.0056	-0.0017	0.0084
2068bp1	2068bp1	Biopsy	d2068	6	#E7298A	2068bp1	0.1469	-0.1962	0.1469	-0.1962	-0.0212	0.0841	0.0009	0.2317	0.1729	0.3203	-0.0461	-0.0259	-0.0482	0.0800	-0.0335	-0.0221	-0.0059	0.0173	-0.0078	-0.0176	0.1024	0.0024	-0.0279	-0.1617	-0.0833	0.0094	0.0410	0.0510	-0.1479	0.0934	-0.2062	0.1249	0.4801	-0.0466	-0.1446	-0.5116	-0.0989	0.1362	-0.0724	0.1031	-0.1117	0.0014	-0.0227	-0.0208	0.0296	0.0002	0.0284	0.0314	0.0036	0.0014	-0.0127	-0.0208	0.0234	-0.0093	-0.0002	-0.0178
2072n1	2072n1	Neutrophils	d2072	8	#D95F02	2072n1	-0.1991	-0.0433	-0.1991	-0.0433	-0.1570	-0.0134	-0.0970	0.0651	0.1829	-0.2062	-0.1483	0.1856	0.0033	0.0381	-0.0011	0.0459	0.1550	0.0594	0.0519	-0.1347	-0.1106	0.0349	0.3795	-0.0720	-0.0286	0.1669	0.0741	-0.0678	0.0837	0.0058	-0.0292	-0.1702	0.1328	0.0628	-0.0586	-0.0333	0.1598	0.0892	-0.0051	-0.0492	0.0447	-0.1530	0.4267	0.3771	-0.2485	0.0012	-0.0415	0.0363	0.0173	0.0494	-0.0073	0.0073	-0.0021	-0.0046	-0.0009	0.0051
2072e1	2072e1	Eosinophils	d2072	8	#66A61E	2072e1	-0.1027	-0.0497	-0.1027	-0.0497	0.2099	0.0079	-0.1356	0.1052	0.1152	-0.2888	0.1691	0.0026	0.1401	0.5573	0.2548	-0.3894	-0.0691	0.0706	-0.1069	0.0826	0.1082	0.1353	-0.1807	-0.0393	0.1363	0.0580	0.1430	-0.0284	-0.0516	0.0353	0.0661	0.1304	0.0151	0.0929	0.0461	0.0024	0.0258	0.0546	0.1448	-0.0294	0.0729	0.0558	0.0827	-0.0394	0.0201	-0.0259	0.0605	-0.0243	0.0235	-0.0498	0.0317	0.0045	0.0015	-0.0010	0.0018	-0.0106
2072bp1	2072bp1	Biopsy	d2072	8	#E7298A	2072bp1	0.1470	-0.1908	0.1470	-0.1908	-0.0343	0.0783	-0.0098	0.3013	0.1428	0.1558	-0.0603	-0.0338	-0.0888	0.0048	0.0022	-0.0105	-0.0850	0.0387	-0.0018	-0.1380	0.0719	-0.0309	0.1356	0.3025	0.1253	-0.1621	0.1004	-0.0852	0.0687	-0.0244	0.2834	-0.1746	-0.4129	-0.0228	0.1423	-0.1244	-0.3084	0.3451	0.1076	-0.0096	0.0446	-0.0860	0.0116	0.0430	0.0526	-0.0293	0.0078	-0.0064	0.0203	0.0004	-0.0178	0.0191	0.0026	0.0126	-0.0113	0.0121
2071bp1	2071bp1	Biopsy	d2071	7	#E7298A	2071bp1	0.1391	-0.1964	0.1391	-0.1964	-0.0284	0.0836	-0.0107	0.3971	0.1990	0.1944	0.0779	0.1393	0.2559	-0.0753	0.0188	0.0704	-0.1222	-0.1725	0.0225	0.1399	-0.1554	0.0125	-0.0001	-0.0428	0.0121	0.0170	0.0374	0.3478	0.0639	-0.1909	0.0496	0.1024	0.0690	0.0478	-0.1917	0.4816	0.0365	-0.1108	-0.0312	-0.0946	0.0824	0.0358	0.0245	0.0026	-0.0017	-0.0379	-0.0380	-0.0184	-0.0042	-0.0082	0.0054	0.0037	0.0246	0.0133	-0.0070	0.0064
2073m1	2073m1	Monocytes	d2073	9	#7570B3	2073m1	0.1625	-0.2026	0.1625	-0.2026	-0.0214	0.1136	0.0270	-0.1409	-0.0731	-0.0852	-0.1060	-0.1057	-0.1435	0.0640	0.0551	-0.0632	0.1457	0.0482	0.0393	0.2786	-0.3629	-0.0633	0.0586	0.1665	0.0313	-0.1353	0.0837	0.0156	-0.0301	0.0864	-0.0032	0.0388	0.0448	0.0062	-0.0121	0.0001	0.0380	-0.0588	-0.0077	0.0082	-0.0182	-0.0140	-0.0113	-0.0003	-0.0042	0.0038	-0.0035	0.0007	0.0027	-0.0013	0.0047	0.0012	-0.0038	-0.0037	0.0030	-0.0045
2073e1	2073e1	Eosinophils	d2073	9	#66A61E	2073e1	-0.0550	0.1364	-0.0550	0.1364	0.2019	0.1989	0.1544	-0.0321	-0.0304	0.0829	-0.1193	0.1275	0.0804	0.0371	0.1318	-0.1308	-0.0179	0.0858	-0.1511	-0.0316	-0.0366	0.0866	0.0930	0.0724	-0.1459	-0.0859	-0.1370	0.0032	0.1087	-0.0918	-0.0873	-0.0829	-0.0163	-0.0652	-0.0407	0.0096	-0.0377	-0.0049	-0.0978	0.1038	0.0314	0.0182	-0.0415	0.0681	0.0006	0.0607	-0.0618	0.1342	-0.5672	-0.3634	-0.3468	-0.0095	-0.0411	-0.0231	0.0114	0.0244
2073bp1	2073bp1	Biopsy	d2073	9	#E7298A	2073bp1	0.1377	-0.1872	0.1377	-0.1872	-0.0353	0.0678	0.0052	0.1560	0.0215	0.1807	0.0978	0.1226	0.0934	0.0896	-0.0416	0.0651	0.0222	-0.0299	-0.0433	-0.1017	0.1297	-0.0241	0.0096	0.0868	-0.0259	-0.0827	-0.0517	-0.3172	-0.0030	0.1048	-0.0485	0.0038	-0.1443	-0.0124	0.3460	-0.1245	0.4540	-0.5310	-0.0083	-0.0281	-0.0086	0.0140	0.0008	0.0069	-0.0504	-0.0254	-0.0588	-0.0246	-0.0301	-0.0001	0.0201	0.0169	0.0153	0.0046	0.0064	0.0036
2068m2	2068m2	Monocytes	d2068	6	#7570B3	2068m2	-0.0079	-0.0554	-0.0079	-0.0554	0.0557	-0.2720	0.1620	-0.1573	-0.0076	0.1754	0.0420	-0.1450	0.0232	-0.0085	-0.0431	0.0054	-0.1480	-0.0103	-0.1119	-0.0373	-0.0761	0.1916	0.0875	-0.1246	0.0623	-0.0602	0.2055	-0.1169	0.2250	0.0845	-0.0328	0.1616	0.1733	0.2544	0.4320	0.1701	-0.1474	0.1321	-0.3934	-0.1257	-0.0113	-0.0033	0.0181	0.0709	-0.0299	-0.0048	0.0271	-0.1060	-0.0582	0.0491	-0.0150	-0.0101	-0.0144	0.0050	0.0070	0.0024
2068n2	2068n2	Neutrophils	d2068	6	#D95F02	2068n2	-0.2008	-0.0452	-0.2008	-0.0452	-0.1766	-0.0026	-0.0600	-0.2073	-0.0022	0.2156	-0.1014	-0.0633	0.0161	0.0532	-0.1376	0.0086	-0.2233	-0.1755	-0.3719	0.1359	0.0313	0.0118	-0.2668	0.3529	0.3069	0.2822	-0.0288	0.0773	0.0225	0.0618	-0.1190	-0.1403	0.0014	-0.2505	-0.0806	-0.0191	0.1278	0.0706	-0.0691	-0.0895	-0.0080	-0.0234	0.1243	0.0693	-0.0234	0.0153	-0.0119	0.0224	-0.0034	0.0033	0.0037	-0.0001	-0.0001	0.0009	-0.0012	-0.0015
2068e2	2068e2	Eosinophils	d2068	6	#66A61E	2068e2	-0.1200	-0.0392	-0.1200	-0.0392	0.2539	0.0276	-0.1064	-0.2229	-0.0795	0.2922	0.1089	-0.2137	-0.0323	-0.0315	-0.1210	0.0865	-0.1455	-0.2214	0.0166	-0.0086	-0.0246	0.1652	0.2388	-0.1572	-0.0942	-0.0159	0.1469	0.0428	0.0244	0.2265	0.0754	0.0952	-0.1182	0.1136	-0.1680	-0.0002	0.1585	0.0347	0.5055	0.1501	0.0472	0.0081	-0.0092	0.1039	-0.0416	-0.0229	0.0198	-0.0403	-0.0072	-0.0974	-0.0185	-0.0106	0.0113	-0.0141	-0.0065	-0.0014
2072m2	2072m2	Monocytes	d2072	8	#7570B3	2072m2	-0.0203	-0.0552	-0.0203	-0.0552	0.0539	-0.2708	0.1209	0.0583	-0.0202	-0.0641	-0.0263	-0.0288	0.0056	0.0559	-0.1315	0.0694	-0.0898	0.1319	-0.0039	-0.0760	-0.0825	0.1116	-0.1164	-0.0712	0.1450	-0.1624	0.1060	-0.0459	0.2303	-0.0212	-0.0156	-0.1946	-0.0338	0.0184	-0.2646	-0.0799	-0.1746	-0.2515	0.0738	-0.0371	-0.1450	0.1070	-0.0240	-0.2513	-0.4449	0.0021	-0.0264	0.3820	0.0896	-0.0209	-0.0401	0.0217	0.0422	-0.0035	-0.0121	-0.0044
2072n2	2072n2	Neutrophils	d2072	8	#D95F02	2072n2	-0.2102	-0.0404	-0.2102	-0.0404	-0.1935	-0.0005	-0.1045	0.0773	0.0232	-0.0979	-0.1550	0.0813	0.0375	0.0399	-0.0912	0.0622	-0.1495	0.1451	0.0582	-0.0629	-0.1345	0.0488	0.1242	0.0544	-0.1487	0.3185	0.2102	0.0069	0.0424	0.1814	-0.1378	-0.1318	0.0009	0.0288	0.0893	0.0526	-0.1535	-0.1651	-0.0045	0.3407	0.2276	-0.0566	-0.1864	-0.4003	0.2181	-0.0631	0.0248	-0.1218	-0.0107	-0.0361	0.0018	0.0150	0.0099	0.0187	-0.0011	0.0052
2072e2	2072e2	Eosinophils	d2072	8	#66A61E	2072e2	-0.1364	-0.0357	-0.1364	-0.0357	0.2362	0.0443	-0.1685	0.1066	-0.0945	-0.0949	0.0237	-0.0439	-0.0632	0.1033	-0.1733	0.0739	-0.1071	0.0215	0.1471	-0.0538	-0.0600	0.1075	0.0226	-0.0088	0.1581	0.0674	-0.1890	0.0536	-0.2266	-0.0074	0.0347	-0.0598	0.0295	0.0311	0.0085	0.0531	-0.0869	-0.1403	-0.1165	-0.1319	-0.2909	-0.5450	-0.3549	0.2016	0.0358	-0.0162	0.0217	0.0201	-0.0391	0.0370	-0.0293	-0.0033	-0.0085	-0.0032	-0.0164	-0.0010
2073m2	2073m2	Monocytes	d2073	9	#7570B3	2073m2	0.0361	0.1227	0.0361	0.1227	0.0234	-0.0747	0.3257	-0.0087	-0.0447	-0.0128	-0.1310	0.2171	-0.0776	0.0939	-0.1652	-0.0979	-0.1126	-0.2370	0.2653	0.2429	0.1938	-0.0079	0.0677	0.0190	0.0538	-0.0046	-0.0327	-0.1069	0.0559	-0.0075	0.0543	0.0808	0.0463	0.0147	0.0212	0.0429	0.0257	-0.0092	-0.0366	0.1531	0.0971	-0.1324	0.1207	0.0607	0.3125	0.0793	0.0172	0.3894	0.3090	-0.1756	-0.0116	-0.0071	-0.0728	-0.0580	0.0066	-0.0059
2073n2	2073n2	Neutrophils	d2073	9	#D95F02	2073n2	-0.1172	0.1370	-0.1172	0.1370	-0.1852	0.1913	0.2542	0.0423	-0.0139	0.0074	0.2305	-0.1814	-0.0537	0.0938	-0.0603	-0.0874	-0.0652	-0.1435	0.1227	-0.2463	-0.2130	-0.2079	-0.2532	-0.0386	-0.0966	-0.0572	-0.0433	-0.0976	0.0973	-0.0662	0.1595	0.1824	0.0014	-0.0986	-0.0583	0.0255	0.0694	0.0719	-0.0766	0.2464	-0.0337	-0.3333	0.1996	-0.1608	-0.2183	-0.0323	0.0436	-0.1715	-0.0430	-0.0310	0.0262	-0.0076	0.0005	-0.0022	0.0014	-0.0036
2073e2	2073e2	Eosinophils	d2073	9	#66A61E	2073e2	-0.0574	0.1392	-0.0574	0.1392	0.1980	0.2064	0.1533	-0.0037	-0.1254	0.1167	-0.1113	0.0979	0.0792	0.0265	0.0737	-0.0949	-0.0738	0.1119	-0.1556	-0.0713	-0.0968	0.1885	0.0673	0.0686	-0.1352	-0.1079	-0.1838	0.0667	0.0255	-0.0550	-0.0884	-0.0129	-0.0073	0.0028	0.0278	0.0135	0.0266	0.0365	0.0664	0.0789	0.0371	-0.0340	0.0747	-0.0904	0.0602	0.1027	-0.0415	0.1144	0.1233	0.7128	0.0997	-0.0039	0.0702	0.0441	0.0333	-0.0080
2068m3	2068m3	Monocytes	d2068	6	#7570B3	2068m3	-0.0260	-0.0573	-0.0260	-0.0573	0.0492	-0.2713	0.1173	0.0412	0.1212	-0.0914	0.0354	0.0226	0.0053	-0.0620	-0.0201	0.0148	-0.0166	0.1350	-0.0821	-0.0026	-0.0200	-0.2320	-0.0790	-0.1376	0.0160	-0.2642	-0.0570	0.1929	-0.1727	0.0676	-0.3224	-0.1359	-0.0291	-0.1728	0.2310	0.1316	0.2877	0.3218	0.1297	0.1421	0.2163	-0.1223	-0.2210	0.0453	-0.1239	-0.1134	0.0564	0.1049	0.0470	-0.0416	-0.0061	0.0395	-0.0006	-0.0009	-0.0089	0.0024
2068n3	2068n3	Neutrophils	d2068	6	#D95F02	2068n3	-0.2086	-0.0418	-0.2086	-0.0418	-0.1802	0.0035	-0.0854	-0.1069	0.1234	-0.0291	-0.1132	0.1101	-0.0221	0.0499	-0.2202	0.0433	-0.0452	-0.0088	-0.2468	0.1215	0.0349	-0.2175	-0.2060	-0.0242	-0.2597	-0.1859	-0.1078	0.0176	-0.2093	-0.1348	0.0279	0.1934	-0.1158	0.3599	0.0618	-0.0398	-0.3325	-0.1826	0.0822	0.0998	0.0802	0.0771	-0.0029	0.2679	-0.0974	0.0545	-0.0320	-0.0021	0.0214	0.0207	-0.0114	0.0020	0.0105	-0.0085	0.0063	0.0031
2068e3	2068e3	Eosinophils	d2068	6	#66A61E	2068e3	-0.1360	-0.0299	-0.1360	-0.0299	0.2543	0.0404	-0.1604	0.0077	0.0074	-0.0510	0.0483	-0.0489	-0.0730	-0.0347	-0.1227	0.0850	0.0621	-0.1250	0.0181	0.0340	0.0820	-0.2668	0.0325	-0.1012	-0.1693	-0.0870	0.1480	0.1501	-0.1490	0.1199	-0.1515	-0.0223	-0.2026	-0.0320	0.0463	-0.0172	-0.0379	0.0051	-0.1761	-0.3465	-0.0591	-0.0603	0.4187	-0.3755	0.1445	0.0864	0.0153	0.1252	-0.1134	0.0233	-0.0650	-0.0079	-0.0309	0.0089	0.0125	0.0057
2072m3	2072m3	Monocytes	d2072	8	#7570B3	2072m3	-0.0265	-0.0540	-0.0265	-0.0540	0.0391	-0.2696	0.1151	0.0625	-0.0240	-0.1087	0.0157	0.0480	-0.0488	0.0013	-0.1538	0.0520	-0.0687	0.1699	0.0043	-0.0517	-0.0617	0.0363	-0.1421	-0.1035	0.1017	-0.2796	0.0107	-0.0647	0.1549	-0.0306	-0.0532	-0.1000	-0.0371	-0.0968	-0.3238	-0.0782	0.0540	-0.1064	0.0279	-0.0153	0.0285	0.0440	0.1424	0.1903	0.4782	0.1049	0.0258	-0.4186	-0.1409	0.0552	0.0582	-0.0430	-0.0010	-0.0002	0.0245	-0.0059
2072n3	2072n3	Neutrophils	d2072	8	#D95F02	2072n3	-0.2143	-0.0400	-0.2143	-0.0400	-0.2139	0.0098	-0.0996	0.0525	-0.0879	-0.0369	-0.0431	0.1031	-0.0256	0.0137	-0.0981	-0.0044	-0.2240	0.2773	0.1155	0.0647	-0.0569	0.0125	0.0464	-0.0296	-0.2819	0.0080	0.0023	-0.0796	0.1351	0.0021	0.1554	0.3842	-0.0597	-0.3259	0.0173	0.0063	0.1720	0.2047	0.0274	-0.2926	-0.2171	0.2167	-0.1903	0.0216	0.0283	0.0013	-0.0029	0.1304	0.0066	-0.0098	-0.0044	-0.0105	-0.0167	-0.0066	-0.0039	-0.0014
2072e3	2072e3	Eosinophils	d2072	8	#66A61E	2072e3	-0.1309	-0.0343	-0.1309	-0.0343	0.2418	0.0343	-0.1613	0.0853	-0.1217	-0.0373	0.0452	-0.0290	-0.0909	-0.0409	-0.1991	0.1585	-0.0934	0.0611	0.2165	-0.0537	-0.1204	0.0620	-0.0017	0.1190	0.2179	-0.0204	-0.3188	-0.0270	-0.2283	-0.1274	0.1975	-0.0333	0.1970	0.0533	0.1282	-0.0284	0.0808	0.1113	-0.1447	0.1720	0.2040	0.4440	0.1635	-0.0975	-0.0899	-0.0159	-0.0414	-0.0508	0.0076	-0.0854	0.0098	0.0047	-0.0064	0.0003	0.0163	0.0035
2159bp1	2159bp1	Biopsy	d2159	10	#E7298A	2159bp1	0.1625	-0.2026	0.1625	-0.2026	-0.0214	0.1136	0.0270	-0.1409	-0.0731	-0.0852	-0.1060	-0.1057	-0.1435	0.0640	0.0551	-0.0632	0.1457	0.0482	0.0393	0.2786	-0.3629	-0.0633	0.0586	0.1665	0.0313	-0.1353	0.0837	0.0156	-0.0301	0.0864	-0.0032	0.0388	0.0448	0.0062	-0.0121	0.0001	0.0380	-0.0588	-0.0077	0.0082	-0.0182	-0.0140	-0.0113	-0.0003	-0.0042	0.0038	-0.0035	0.0007	0.0027	-0.0013	0.0047	0.0012	-0.0038	-0.0037	0.0030	-0.0045
2073m3	2073m3	Monocytes	d2073	9	#7570B3	2073m3	0.0326	0.1286	0.0326	0.1286	0.0381	-0.0793	0.3241	0.0184	-0.0078	-0.0634	-0.2184	0.1798	-0.0265	0.1112	-0.0964	-0.0676	-0.0538	-0.2159	0.2864	0.2020	0.2107	-0.0857	0.0787	0.0722	0.0095	0.1100	0.0387	0.0871	-0.0994	0.0772	-0.0289	-0.0518	-0.0384	0.0319	0.0138	-0.0458	-0.0184	0.0439	0.0971	-0.1440	-0.1063	0.1443	-0.1207	-0.0690	-0.3172	-0.0764	-0.0221	-0.4074	-0.2526	0.1709	0.0352	-0.0004	0.0727	0.0537	-0.0156	0.0054
2073n3	2073n3	Neutrophils	d2073	9	#D95F02	2073n3	-0.1125	0.1399	-0.1125	0.1399	-0.1536	0.1795	0.2418	0.0301	0.0757	-0.0382	0.0785	-0.1685	0.0065	0.1238	0.0156	0.0163	0.1257	-0.2275	0.1081	-0.3795	-0.2367	-0.0959	-0.0610	-0.0557	0.1082	0.0786	0.1266	0.0688	-0.1146	0.0725	-0.0809	-0.1417	0.0037	0.0786	0.0596	-0.0227	-0.0278	-0.0342	0.0686	-0.2452	0.0296	0.3494	-0.2296	0.1902	0.2334	0.0797	-0.0534	0.2048	0.0032	0.0443	-0.0393	-0.0010	0.0010	0.0008	-0.0005	0.0049
2073e3	2073e3	Eosinophils	d2073	9	#66A61E	2073e3	-0.0637	0.1451	-0.0637	0.1451	0.2006	0.2129	0.1492	0.0029	-0.0544	0.0684	-0.1611	0.0997	0.0600	-0.0730	0.0615	0.0000	0.0327	0.1174	-0.1491	-0.1117	-0.0804	0.0348	0.0048	0.0485	-0.0983	-0.0407	-0.0531	0.0432	0.0193	-0.0169	-0.1444	-0.0672	0.0104	0.0029	0.0367	-0.0054	-0.0843	-0.0414	0.0366	-0.2210	-0.1293	0.0312	0.0473	-0.0173	-0.0387	-0.2039	0.1572	-0.2784	0.4743	-0.4234	0.2423	-0.0046	-0.0398	-0.0083	-0.0250	-0.0089
2162m1	2162m1	Monocytes	d2162	11	#7570B3	2162m1	0.0001	-0.0628	0.0001	-0.0628	0.0579	-0.2750	0.1418	-0.0963	0.2187	0.0398	0.1062	-0.0309	0.0486	-0.2242	0.2081	-0.1019	-0.0379	0.1337	0.1567	-0.0694	-0.0837	0.0951	-0.0784	0.2649	-0.1496	0.2460	-0.0922	0.0331	-0.1820	-0.0072	-0.0499	0.1210	-0.2956	0.3634	-0.2544	-0.1747	0.2149	0.0648	-0.2036	-0.0080	-0.0413	-0.0187	-0.0209	-0.0226	0.0349	-0.0296	-0.0040	0.0508	0.0523	-0.0223	-0.0217	0.0020	-0.0101	0.0010	0.0025	-0.0002
2162n1	2162n1	Neutrophils	d2162	11	#D95F02	2162n1	-0.1781	-0.0555	-0.1781	-0.0555	-0.1270	-0.0244	-0.0366	-0.1594	0.2184	0.0405	-0.0847	0.1052	0.0399	-0.0676	0.0793	0.0188	0.3902	-0.1230	0.1698	-0.0708	0.1200	0.5016	-0.1811	-0.0054	-0.0085	-0.2492	-0.0180	0.1963	-0.1163	0.2182	0.1616	0.0616	-0.0664	-0.2843	0.0672	0.0654	-0.0933	-0.0648	-0.1015	0.0970	-0.0167	-0.0032	0.0179	-0.0316	-0.0251	0.0094	0.0331	-0.0258	0.0124	-0.0121	0.0085	-0.0130	0.0059	-0.0030	0.0048	-0.0025
2162e1	2162e1	Eosinophils	d2162	11	#66A61E	2162e1	-0.1247	-0.0397	-0.1247	-0.0397	0.2461	0.0302	-0.1423	0.0170	0.1307	-0.0514	0.0643	0.0047	-0.0557	-0.2627	0.0509	0.0748	0.1814	-0.0712	0.2497	0.0495	0.0568	-0.0388	-0.3315	0.2886	-0.0862	0.0789	0.0938	-0.1907	0.3622	-0.1853	-0.2333	0.0515	0.2273	0.0168	0.1543	0.0182	-0.0861	0.0421	0.2887	-0.0507	0.0225	-0.0656	-0.0527	0.0497	0.0163	0.0414	-0.0870	0.0163	-0.0472	0.0553	0.0000	-0.0011	0.0186	0.0067	-0.0049	-0.0036
2162bp1	2162bp1	Biopsy	d2162	11	#E7298A	2162bp1	0.1555	-0.2072	0.1555	-0.2072	-0.0303	0.1488	0.0221	0.0070	0.0316	-0.4237	-0.2222	-0.1965	-0.2877	-0.3823	0.0881	-0.2149	-0.3376	-0.2138	-0.1482	-0.1776	0.1816	0.1675	-0.0229	-0.1409	-0.0526	0.0109	-0.0017	0.0540	-0.0216	-0.0978	0.0263	0.0159	0.0493	-0.0397	0.0386	-0.0034	0.0807	-0.1159	0.0042	-0.0187	0.0353	0.0298	0.0043	-0.0040	-0.0161	-0.0176	-0.0031	0.0029	-0.0112	0.0002	-0.0020	0.0081	-0.0060	0.0013	-0.0004	0.0011
macrofagos	Macrofagos	macrophage	unknown	12	#E6AB02	Macrofagos	0.1444	0.1680	0.1444	0.1680	-0.0254	-0.0492	-0.0944	-0.1309	0.0190	0.0830	-0.0898	-0.0310	-0.0362	0.1539	0.1875	0.2545	-0.1047	-0.0188	0.0685	-0.0034	-0.0112	0.0854	0.0016	-0.0323	-0.0853	-0.0219	0.1315	-0.0413	-0.1053	-0.2945	0.0491	-0.0056	0.0107	-0.0952	-0.0477	-0.1184	0.0394	-0.0244	-0.0456	-0.1900	0.3862	-0.1438	-0.1197	-0.0412	-0.1164	0.3838	0.1213	-0.0040	-0.0594	-0.0765	0.2958	0.1776	-0.1207	0.1031	0.0900	0.1495
macrofagos+sbv	Macrofagos+SbV	macrophage	unknown	12	#E6AB02	Mcrfgs+SbV	0.1387	0.1752	0.1387	0.1752	-0.0294	-0.0424	-0.1192	-0.0897	0.0458	0.0262	-0.1691	-0.2171	0.1909	0.0324	-0.0517	-0.0029	0.0052	0.0483	0.0757	-0.0036	0.0430	-0.0060	0.0116	-0.0161	-0.0338	-0.0215	0.1150	-0.0746	-0.1105	-0.2196	0.0004	-0.0385	-0.0281	-0.0548	0.0190	0.0516	0.0254	-0.0023	-0.0254	0.0689	-0.0700	-0.0056	0.0575	0.0359	0.0795	-0.2255	-0.0766	0.1264	-0.1308	-0.0555	0.2497	-0.2497	0.3375	0.1343	0.1437	-0.5451
macrofagos+10772	Macrofagos+10772	macrophage	unknown	12	#E6AB02	Mcrf+10772	0.1408	0.1691	0.1408	0.1691	-0.0438	-0.0405	-0.1069	-0.0383	-0.0142	0.0196	0.0725	0.1159	-0.1593	0.0675	0.1024	0.1331	-0.0442	-0.0168	-0.0282	-0.0070	-0.0244	0.0566	-0.0253	0.0046	-0.0324	0.0029	0.1539	0.0056	-0.0894	-0.1813	-0.0056	-0.0536	-0.0077	-0.0420	0.0311	-0.0017	0.0605	-0.0028	0.0042	-0.0146	0.0140	0.0015	-0.0365	-0.0395	-0.0651	0.1174	0.0612	-0.1607	0.2498	0.0659	-0.5295	-0.5485	0.0002	-0.1839	-0.1245	-0.0953
macrofagos+10772+sbv	Macrofagos+10772+SbV	macrophage	unknown	12	#E6AB02	M+10772+SV	0.1362	0.1762	0.1362	0.1762	-0.0361	-0.0374	-0.1206	-0.0888	0.0024	0.0309	-0.1061	-0.1709	0.1540	0.0098	-0.1121	-0.0947	0.0529	0.0535	0.0589	-0.0045	0.0277	0.0128	-0.0063	-0.0307	-0.0148	-0.0264	0.0400	-0.0590	-0.0526	-0.1432	0.0123	0.0157	0.0151	-0.0548	-0.0227	-0.0076	0.0159	-0.0208	-0.0194	-0.0517	0.0635	-0.0292	0.0527	0.0028	0.0900	-0.2490	-0.0957	-0.0163	0.0675	0.0263	-0.1941	0.2727	0.4227	-0.0818	-0.4098	0.4632
macrofagos+2169	Macrofagos+2169	macrophage	unknown	12	#E6AB02	Mcrfg+2169	0.1350	0.1637	0.1350	0.1637	-0.0589	-0.0294	-0.0918	-0.0602	-0.0668	0.0625	0.2523	0.2587	-0.2778	-0.0236	-0.0448	-0.0718	0.0222	-0.0030	-0.0634	-0.0080	-0.0476	0.0932	-0.0295	-0.0253	-0.0116	0.0326	0.1741	0.0119	-0.0985	-0.1325	-0.0142	-0.0574	0.0104	-0.0291	0.0032	0.0226	-0.0214	-0.0008	0.0205	0.0230	-0.1061	0.0285	0.0292	0.0150	0.0391	-0.2727	-0.0955	-0.0348	0.0663	0.0367	-0.2292	0.4414	-0.0524	0.2161	0.4568	-0.0630
macrofagos+2169+sbv	Macrofagos+2169+SbV	macrophage	unknown	12	#E6AB02	Mc+2169+SV	0.1307	0.1729	0.1307	0.1729	-0.0525	-0.0229	-0.1276	0.0221	-0.0264	0.0160	0.0704	-0.0233	0.0996	-0.1239	-0.2168	-0.2743	0.1093	0.0198	-0.0137	0.0006	-0.0232	0.0115	0.0415	-0.0012	0.0226	0.0081	-0.1280	0.0116	0.0885	0.1273	0.0395	0.0428	0.0239	-0.0052	-0.0634	-0.0985	-0.0567	-0.0397	-0.0011	-0.2170	0.3410	-0.0641	-0.0790	-0.0361	-0.0687	-0.0222	-0.0271	-0.0521	-0.0072	0.0595	-0.0453	0.2132	-0.2808	-0.3581	-0.1836	-0.4549
macrofagos+12309	Macrofagos+12309	macrophage	unknown	12	#E6AB02	Mcrf+12309	0.1409	0.1700	0.1409	0.1700	-0.0348	-0.0319	-0.1139	-0.0270	0.0459	-0.0560	-0.0447	0.0337	-0.1054	0.1016	0.2571	0.2857	-0.1105	-0.0477	-0.0035	-0.0168	0.0082	-0.0777	-0.0651	-0.0287	0.0253	-0.0420	-0.2342	0.0302	0.1695	0.2720	0.0321	0.0807	0.0263	0.0575	-0.0508	-0.0175	-0.0505	-0.0128	-0.0030	-0.0232	0.0497	-0.0070	0.0426	0.0195	0.0580	-0.2945	-0.1153	0.0588	-0.0289	0.0433	-0.0342	-0.0430	-0.2389	0.4888	-0.3417	-0.0732
macrofagos+12309+sbv	Macrofagos+12309+SbV	macrophage	unknown	12	#E6AB02	M+12309+SV	0.1383	0.1749	0.1383	0.1749	-0.0349	-0.0349	-0.1333	0.0010	0.0613	-0.0138	-0.1397	-0.1868	0.2198	-0.0082	-0.0582	-0.0235	0.0080	0.0221	0.0447	0.0067	0.0304	-0.0240	-0.0155	0.0049	0.0063	-0.0284	0.0600	-0.0318	-0.0433	-0.0584	-0.0299	-0.0345	-0.0113	-0.0031	0.0146	0.0469	0.0164	0.0009	0.0300	0.1338	-0.2087	0.0615	0.0440	0.0125	0.0224	-0.2137	-0.0818	0.0319	-0.0664	0.0961	0.1115	-0.1847	-0.6051	-0.2373	0.2225	0.3567
macrofagos+12367+sbv	Macrofagos+12367+SbV	macrophage	unknown	12	#E6AB02	M+12367+SV	0.1352	0.1763	0.1352	0.1763	-0.0425	-0.0304	-0.1474	0.0987	0.0592	-0.0754	-0.1129	-0.1740	0.2262	-0.0695	-0.0535	-0.0480	0.0174	0.0111	0.0070	0.0115	0.0245	-0.0606	0.0266	0.0415	0.0372	-0.0012	-0.0413	0.0218	0.0314	0.0901	-0.0630	-0.0036	-0.0216	0.0431	0.0787	0.0920	0.0643	0.0395	0.0303	0.2158	-0.3629	0.1031	0.0322	0.0162	-0.0195	0.5324	0.2109	-0.0973	0.1246	-0.0482	-0.1827	0.2771	-0.0374	0.2479	-0.0596	-0.1237
macrofagos+1126	Macrofagos+1126	macrophage	unknown	12	#E6AB02	Mcrfg+1126	0.1390	0.1714	0.1390	0.1714	-0.0368	-0.0313	-0.1229	0.0372	0.0523	-0.0895	-0.0550	0.0142	-0.0743	0.0632	0.2546	0.2683	-0.1003	-0.0558	-0.0186	-0.0166	0.0075	-0.0965	-0.0304	0.0022	0.0372	-0.0070	-0.2546	0.0556	0.1815	0.3185	0.0031	0.0754	-0.0009	0.0786	-0.0050	0.0196	-0.0380	0.0261	-0.0026	0.0007	-0.0482	0.0073	0.0142	-0.0032	0.0178	0.0203	0.0108	0.0034	-0.0151	-0.0222	0.0304	0.0920	0.3535	-0.4870	0.3674	0.0373
macrofagos+12251	Macrofagos+12251	macrophage	unknown	12	#E6AB02	Mcrf+12251	0.1360	0.1627	0.1360	0.1627	-0.0653	-0.0250	-0.1059	0.0180	-0.0439	0.0124	0.2943	0.2953	-0.2828	-0.0718	-0.0159	-0.0715	-0.0081	-0.0221	-0.1029	-0.0014	-0.0686	0.0770	0.0102	0.0214	-0.0023	0.0422	0.1125	0.0611	-0.0599	-0.0120	-0.0623	-0.0804	-0.0274	0.0432	0.0701	0.0625	-0.0180	0.0402	0.0062	0.1722	-0.2602	0.0857	0.0355	0.0206	0.0131	0.1011	0.0486	0.1104	-0.2074	-0.0473	0.4506	-0.0390	0.0432	-0.1815	-0.4108	0.0403
macrofagos+12251+sbv	Macrofagos+12251+SbV	macrophage	unknown	12	#E6AB02	M+12251+SV	0.1298	0.1715	0.1298	0.1715	-0.0629	-0.0169	-0.1310	0.0693	-0.0426	-0.0197	0.1523	0.0566	0.0192	-0.1831	-0.2342	-0.3226	0.1286	0.0255	-0.0676	0.0063	-0.0242	-0.0109	0.0503	0.0126	0.0645	0.0307	-0.1315	0.0262	0.0986	0.2230	0.0238	0.0489	0.0218	0.0392	-0.0319	-0.0498	-0.0451	-0.0055	0.0038	-0.1247	0.2055	-0.0499	-0.0762	-0.0107	-0.0652	0.1185	0.0378	0.0308	-0.0040	-0.0762	0.0808	-0.4001	0.1804	0.3438	0.2588	0.3049

write.csv(q2_pca$table, file="q2_pca_coords.csv")

if (!isTRUE(get0("skip_load"))) {
  pander::pander(sessionInfo())
  message(paste0("This is hpgltools commit: ", get_git_commit()))
  message(paste0("Saving to ", savefile))
  tmp <- sm(saveme(filename=savefile))
}

## If you wish to reproduce this exact build of hpgltools, invoke the following:

## > git clone http://github.com/abelew/hpgltools.git

## > git reset 4f025ebdf7b19ddfef0cf9ddaa9ebe2857477394

## This is hpgltools commit: Wed Aug 19 10:11:52 2020 -0400: 4f025ebdf7b19ddfef0cf9ddaa9ebe2857477394

## Saving to 01_annotation_v202009.rda.xz

tmp <- loadme(filename=savefile)