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

Description Usage Arguments Examples

View source: R/plot.pathwayMap.r

Description

Generate pathway map with patient perturbation data superimposed.

Usage

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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

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

BRL-BCM/CTD documentation built on Feb. 7, 2020, 1:42 a.m.