plotGeneSetSignificance: Plot the Significance for the Genes of a Given Gene Set

In MLP: MLP

Description

Plot the Significance for the Genes of a Given Gene Set

Usage

plotGeneSetSignificance(geneSet, geneSetIdentifier, geneStatistic,
  annotationPackage, barColors = NULL, descriptionInMainTitle = TRUE)

Arguments

geneSet	object of class 'geneSetMLP' as produced by function getGeneSets
geneSetIdentifier	identifier of the gene set for which a significance plot should be produced; character of length one
geneStatistic	named vector of gene statistics (e.g. p values); the names of the vector are Entrez Gene identifiers
annotationPackage	name of the annotation package to be used (without .db extension); character of length one
barColors	named vector of colors to use for the bars of the barplot; the names of the vector are Entrez Gene identifiers and the vector should be of length equal to the length of the geneStatistic vector defaults to NULL in which case 'grey50' is used
descriptionInMainTitle	Boolean whether or not to use the gene set description in the main title of the plot

Value

no return value

Examples

pathExamplePValues <- system.file("exampleFiles", "examplePValues.rda", package = "MLP")
pathExampleGeneSet <- system.file("exampleFiles", "exampleGeneSet.rda", package = "MLP")
pathExampleMLPResult <- system.file("exampleFiles", "exampleMLPResult.rda", package = "MLP")
load(pathExampleGeneSet)
load(pathExamplePValues)
load(pathExampleMLPResult) 
# annotationPackage <- if (require(mouse4302mmentrezg.db)) "mouse4302mmentrezg" else "mouse4302"
annotationPackage <- "mouse4302"
geneSetID <- rownames(exampleMLPResult)[1]
dev.new(width = 10, height = 10)
op <- par(mar = c(25, 10, 6, 2))
plotGeneSetSignificance(
    geneSet = exampleGeneSet, 
    geneSetIdentifier = geneSetID, 
    geneStatistic = examplePValues, 
    annotationPackage = annotationPackage
)
par(op)

MLP documentation built on Nov. 8, 2020, 8:23 p.m.