plot.pathwayMap: Generate pathway map with patient perturbation data...

In BRL-BCM/CTDext: Extension package for the CTD R package.

Generate pathway map with patient perturbation data superimposed.

Description

Generate pathway map with patient perturbation data superimposed.

Usage

plot.pathwayMap(Pathway, ptID, pt.zscore, zscore.threshold, scale, out.path, SVG=TRUE)

Arguments

Pathway	- The name of the pathway map you want to plot patient data on.
ptID	- An identifier string associated with the patient.
pt.zscore	- A named vector of metabolites with corresponding z-scores.
zscore.threshold	- Plot all z-scores > or < this threshold.
scale	- Integer associated with increase in node size.
out.path	- The directory in which you want to store image files.
SVG	- Save as SVG or PNG? If SVG is TRUE, then an SVG image is saved. If FALSE, a PNG is saved.

Examples

require(CTD)
data(Miller2015)
Miller2015 = Miller2015[-1,grep("IEM", colnames(Miller2015))]
ptID = colnames(Miller2015)[1]
pt.zscore = Miller2015[,1]
Pathway = pathway.ListMaps_metabolon()
plot.pathwayMap(Pathway[1], ptID, pt.zscore, zscore.threshold, scale=1, out.path=getwd(), SVG=TRUE)

BRL-BCM/CTDext documentation built on May 7, 2022, 5:31 a.m.