sample_sheet <- "sample_sheets/dda_samples.xlsx"
savefile <- "mzxml_dda_data_201805.rda"

metadata <- openxlsx::read.xlsx(sample_sheet)
keeper_idx <- metadata[["sampledate"]] == "20180420"
metadata <- metadata[keeper_idx, ]

knitr::kable(metadata)

if (file.exists(savefile)) {
  load(savefile)
} else {
  mzxml_data <- sm(extract_mzxml_data(metadata,
                                      file_column="mzxmlfile",
                                      savefile=savefile))
}

intensity_boxplot <- sm(plot_mzxml_boxplot(mzxml_data))
pp(file="images/mzxml_intensities.png", image=intensity_boxplot)

## Writing the image to: images/mzxml_intensities.png and calling dev.off().

retention_boxplot <- sm(plot_mzxml_boxplot(mzxml_data, table="scans", column="peakscount"))
pp(file="images/mzxml_retention.png", image=retention_boxplot)

## Writing the image to: images/mzxml_retention.png and calling dev.off().

mz_boxplot <- sm(plot_mzxml_boxplot(mzxml_data, table="scans", column="basepeakmz"))
pp(file="images/mzxml_mzbase.png", image=mz_boxplot)

## Writing the image to: images/mzxml_mzbase.png and calling dev.off().

scanintensity_boxplot <- sm(plot_mzxml_boxplot(mzxml_data, table="scans", column="basepeakintensity"))
pp(file="images/mzxml_scanintensity.png", image=scanintensity_boxplot)

## Writing the image to: images/mzxml_scanintensity.png and calling dev.off().

intensity_wrt_mz <- sm(plot_intensity_mz(mzxml_data, x_scale="log", y_scale="log"))
pp(file="images/intensity_wrt_mz_dia.png", image=intensity_wrt_mz$plot)

## Writing the image to: images/intensity_wrt_mz_dia.png and calling dev.off().

## Warning in guide_merge.legend(init, x[[i]]): Duplicated override.aes is
## ignored.

## Warning in guide_merge.legend(init, x[[i]]): Duplicated override.aes is
## ignored.

sample_sheet <- "sample_sheets/Mtb_dia_samples.xlsx"
savefile <- "mzxml_dia_data_201805.rda"

metadata <- openxlsx::read.xlsx(sample_sheet)
keeper_idx <- metadata[["expt_id"]] == "may2018"
keeper_idx[is.na(keeper_idx)] <- FALSE
metadata <- metadata[keeper_idx, ]
knitr::kable(metadata)

if (file.exists(savefile)) {
  load(savefile)
} else {
  mzxml_data <- sm(extract_mzxml_data(metadata,
                                      file_column="Filename",
                                      savefile=savefile))
}

intensity_boxplot <- plot_mzxml_boxplot(mzxml_data)

## Adding 2018_0502BrikenDIA07

## Adding 2018_0502BrikenDIA08

## Adding 2018_0502BrikenDIA09

## Adding 2018_0502BrikenDIA10

## Adding 2018_0502BrikenDIA11

## Adding 2018_0502BrikenDIA12

## Adding 2018_0502BrikenDIA01

## Adding 2018_0502BrikenDIA02

## Adding 2018_0502BrikenDIA03

## Adding 2018_0502BrikenDIA04

## Adding 2018_0502BrikenDIA05

## Adding 2018_0502BrikenDIA06

## 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 213990 zero count features.

pp(file="images/201805_dia_mzxml_intensities.png", image=intensity_boxplot)

## Writing the image to: images/201805_dia_mzxml_intensities.png and calling dev.off().

retention_boxplot <- plot_mzxml_boxplot(mzxml_data, table="scans", column="peakscount")

## Adding 2018_0502BrikenDIA07

## Adding 2018_0502BrikenDIA08

## Adding 2018_0502BrikenDIA09

## Adding 2018_0502BrikenDIA10

## Adding 2018_0502BrikenDIA11

## Adding 2018_0502BrikenDIA12

## Adding 2018_0502BrikenDIA01

## Adding 2018_0502BrikenDIA02

## Adding 2018_0502BrikenDIA03

## Adding 2018_0502BrikenDIA04

## Adding 2018_0502BrikenDIA05

## Adding 2018_0502BrikenDIA06

pp(file="images/201805_dia_mzxml_retention.png", image=retention_boxplot)

## Writing the image to: images/201805_dia_mzxml_retention.png and calling dev.off().

mz_boxplot <- plot_mzxml_boxplot(mzxml_data, table="scans", column="basepeakmz")

## Adding 2018_0502BrikenDIA07

## Adding 2018_0502BrikenDIA08

## Adding 2018_0502BrikenDIA09

## Adding 2018_0502BrikenDIA10

## Adding 2018_0502BrikenDIA11

## Adding 2018_0502BrikenDIA12

## Adding 2018_0502BrikenDIA01

## Adding 2018_0502BrikenDIA02

## Adding 2018_0502BrikenDIA03

## Adding 2018_0502BrikenDIA04

## Adding 2018_0502BrikenDIA05

## Adding 2018_0502BrikenDIA06

pp(file="images/201805_dia_mzxml_mzbase.png", image=mz_boxplot)

## Writing the image to: images/201805_dia_mzxml_mzbase.png and calling dev.off().

scanintensity_boxplot <- plot_mzxml_boxplot(mzxml_data, table="scans", column="basepeakintensity")

## Adding 2018_0502BrikenDIA07

## Adding 2018_0502BrikenDIA08

## Adding 2018_0502BrikenDIA09

## Adding 2018_0502BrikenDIA10

## Adding 2018_0502BrikenDIA11

## Adding 2018_0502BrikenDIA12

## Adding 2018_0502BrikenDIA01

## Adding 2018_0502BrikenDIA02

## Adding 2018_0502BrikenDIA03

## Adding 2018_0502BrikenDIA04

## Adding 2018_0502BrikenDIA05

## Adding 2018_0502BrikenDIA06

pp(file="images/201805_dia_mzxml_scanintensity.png", image=scanintensity_boxplot)

## Writing the image to: images/201805_dia_mzxml_scanintensity.png and calling dev.off().

intensity_wrt_mz <- plot_intensity_mz(mzxml_data, x_scale="log", y_scale="log")

## Adding 2018_0502BrikenDIA07

## Adding 2018_0502BrikenDIA08

## Adding 2018_0502BrikenDIA09

## Adding 2018_0502BrikenDIA10

## Adding 2018_0502BrikenDIA11

## Adding 2018_0502BrikenDIA12

## Adding 2018_0502BrikenDIA01

## Adding 2018_0502BrikenDIA02

## Adding 2018_0502BrikenDIA03

## Adding 2018_0502BrikenDIA04

## Adding 2018_0502BrikenDIA05

## Adding 2018_0502BrikenDIA06

pp(file="images/201805_dia_intensity_wrt_mz_dia.png", image=intensity_wrt_mz)

## Writing the image to: images/201805_dia_intensity_wrt_mz_dia.png and calling dev.off().

## Warning in guide_merge.legend(init, x[[i]]): Duplicated override.aes is
## ignored.

## Warning in guide_merge.legend(init, x[[i]]): Duplicated override.aes is
## ignored.

export type="whole"
./transition_library_201805.sh 2>&1 1>transition_library_hcd_201805.out
cat transition_library_hcd_201805.out

export type="whole"
./dia_invocation_hcd_201805.sh 2>&1 1>openswath_invocation_201805.out

export type="cf"
./transition_library_201805.sh 2>&1 1>transition_library_hcd_201805.out
cat transition_library_hcd_201805.out

./dia_invocation_hcd_201805.sh 2>&1 1>openswath_invocation_201805.out

if (!isTRUE(get0("skip_load"))) {
  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))
  pander::pander(sessionInfo())
}

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

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

## > git reset 8de6008c66ed31502abbdef703c69345f86a6eed

## R> packrat::restore()

## This is hpgltools commit: Thu May 17 11:08:19 2018 -0400: 8de6008c66ed31502abbdef703c69345f86a6eed

## Saving to 01_preprocessing_comet_20180508-v20180215.rda.xz

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