Plot the Significance for the Genes of a Given Gene Set

Description

Plot the Significance for the Genes of a Given Gene Set

Usage

1
2
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
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)