plotExpressionProfiles {geNetClassifier} | R Documentation

## Expression profiles plot.

### Description

Plots the expression profiles of the given genes.

### Usage

    plotExpressionProfiles(eset, genes=NULL, fileName=NULL,
    geneLabels=NULL, type="lines", sampleLabels=NULL, sampleColors=NULL,
    labelsOrder=NULL, classColors=NULL, sameScale=TRUE,
    showSampleNames=FALSE, showMean= FALSE, identify=TRUE, verbose=TRUE)

### Arguments

`eset` | ExpressionSet or Matrix. Gene expression of the samples.
`genes` | Vector or Matrix. IDs of the genes to plot. If matrix: genes should be ordered by classes. Columns should be named after the classes. If not provided, all available genes will be plot. Warning: If a list of genes is not provided, it will plot all available genes.
`fileName` | Character. File name to save the plots. If not provided, up to 20 genes will be shown on screen.
`geneLabels` | Vector or Matrix. Gene name, ID or label which should be shown in the returned results and plots.
`type` | Character. Plot type: "lines" or "boxplot".
`sampleLabels` | Character. PhenoData variable (column name) containing the train samples class labels. Matrix or Factor. Class labels of the train samples.
`sampleColors` | Character. Colors for the lines of the samples.
`labelsOrder` | Vector or Factor. Order in which the labels should be shown in the returned results and plots.
`classColors` | Character. Colors for each of the classes or samples of the class. Provide either sampleColors or classColors, not both.
`sameScale` | Logical. If TRUE, plots all the genes in the same expression scale.
`showSampleNames` | Logical. If TRUE, the sample names are shown in the plot. Not recommended for big datasets.
`showMean` | Logical. If TRUE, plots the class expression mean.
`identify` | Logical. If TRUE and supported (X11 or quartz devices), the plot will be interactive and clicking on a point will identify the sample the point represents. Press ESC or right-click on the plot screen to exit.
`verbose` | Logical. If TRUE, a message indicating where the pdf is saved will be printed on screen.

### Value

The expression profiles plot, saved in the working directory as 'fileName.pdf'.

### Author(s)

Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain

### Examples

    ######
    # Load libraries and expression data
    ######

    # Load an expressionSet:
    library(leukemiasEset)
    data(leukemiasEset)

    ######
    # Generic expression profile plot
    ######
    # Plot expression of specific genes:
    selectedGenes <- c("ENSG00000169575","ENSG00000078399","ENSG00000005381","ENSG00000154511")
    plotExpressionProfiles(leukemiasEset, genes=selectedGenes, sampleLabels="LeukemiaType", type="boxplot")

    # Color samples:
    plotExpressionProfiles(leukemiasEset, genes="ENSG00000078399",
     sampleLabels="LeukemiaType",
     showMean=TRUE, identify=FALSE,
     sampleColors=c("grey","red")
     [(sampleNames(leukemiasEset) %in% c("GSM331386.CEL","GSM331392.CEL"))+1])

    # Color classes:
    plotExpressionProfiles(leukemiasEset, genes="ENSG00000078399",
     sampleLabels="LeukemiaType",
     showMean=TRUE, identify=TRUE,
     classColors=c("red", "blue", "red", "red","red"))

    ######
    # Expression profiles related to a classifier
    ######
    # Train a classifier or load a trained one:
    trainSamples<- c(1:10, 13:22, 25:34, 37:46, 49:58)
    # summary(leukemiasEset$LeukemiaType[trainSamples])
    # leukemiasClassifier <- geNetClassifier(leukemiasEset[,trainSamples],
    #    sampleLabels="LeukemiaType", plotsName="leukemiasClassifier")
    data(leukemiasClassifier) # Sample trained classifier

    # Plot expression of the selected genes in the train samples:
    plotExpressionProfiles(leukemiasEset[,trainSamples], leukemiasClassifier,
        sampleLabels="LeukemiaType", fileName="leukExprs.pdf")

    # Plot expression of all the genes of specific classes:
    classGenes <- getRanking(leukemiasClassifier@classificationGenes,
        showGeneID=TRUE)$geneID[,c("CLL"), drop=FALSE] # Feel free to modify
    plotExpressionProfiles(leukemiasEset, genes=classGenes, sampleLabels="LeukemiaType",
        type="boxplot")

    # Plot (on screen) the expression of the top ranked genes of each class
    plotExpressionProfiles(leukemiasEset, leukemiasClassifier, sampleLabels="LeukemiaType")

[Package geNetClassifier version 1.30.0 Index]