plotIsoDiffReport: Plot output of getIsoDiffReport()

In yufree/x13cms: Untargeted isotope-based metabolomics

Plot output of getIsoDiffReport()

Description

Generates bar plots comparing isotopologue distributions in labeled samples of two different sample conditions. Use relative ion intensities to show distributions.

Usage

plotIsoDiffReport(isoDiffReport, xcmsSet, intChoice, sampleNames1, sampleNames2, labelReport1, labelReport2, classes1, classes2, labeledSamples, isotopeMassDifference, outputfile)

Arguments

isoDiffReport	Output of getIsoDiffReport().
xcmsSet	xcmsSet object containing grouped and retention-time-aligned peaks (i.e. after calling group() and retcor() in XCMS)
intChoice	"intChoice" from getIsoLabelReport()
sampleNames1	"sampleNames" from getIsoLabelReport() called for condition 1
sampleNames2	"sampleNames" from getIsoLabelReport() called for condition 2
labelReport1	output of getIsoLabelReport() for condition 1
labelReport2	output of getIsoLabelReport() for condition 2
classes1	character vector designating whether each sample in labelsReport1 is unlabeled or labeled
classes2	character vector designating whether each sample in labelsReport2 is unlabeled or labeled
labeledSamples	character variable designating labeled samples (e.g. "C13")
isotopeMassDifference	mass difference between unlabeled and labeled atom, e.g. 1.00335 for C13
outputfile	Name of pdf file to which plots are drawn.

Value

Pdf file containing 12 comparison plots per page.

Author(s)

Xiaojing Huang

Examples

## Not run:
## plotIsoDiffReport(isoDiffReport, "isoDiffPlots.pdf") 

yufree/x13cms documentation built on Feb. 7, 2024, 3:24 p.m.