plotGeneSetSignificance {MLP} | R Documentation

## Plot the Significance for the Genes of a Given Gene Set

### 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)

[Package MLP version 1.42.0 Index]