caOmicsV (version 1.2.0)

plotBioMatrixHeatmap: Heatmap Plot on caOmicsV bioMatrix Layout

Description

Headmap plot method for bioMatrix layout. This function will plot all rows of the input data. bioMatrix layout and graphic device must be initialized first.

Usage

plotBioMatrixHeatmap(exprData, topAdjust=0, bottomAdjust=0,  maxValue=NULL, minValue=NULL,  heatmapColor="BlueWhiteRed", skipPlotRow=0)

Arguments

exprData

numeric matrix (log2 values) with row names

topAdjust

non-negative numeric, height of top y coordinate should be reduced to show different layers, default 0

bottomAdjust

non-negative numeric, height of bottom y coordinate should be reduced for a small rectangle, default 0

maxValue

numeric, value for highest color in heatmap, set to NULL to use the maximum value in expression dataset

minValue

numeric, value for lowest color in heatmap, set to NULL to use the minimum value in expression dataset

heatmapColor

character vector,one of "BlueWhiteRed", "GreenWhiteRed", "GreenYellowRed", "GreenBlackRed" , or "YellowToRed"

skipPlotRow

non-negative integer, total rows on plot area that should be skipped, default 0

Value

None

Examples

    initializeBioMatrixPlot(numOfGenes=1, numOfSamples=50)
    showBioMatrixPlotLayout("Gene", paste("Sample", 1:50),  "Diagnosis")

    data(biomatrixPlotDemoData)
    exprData <- biomatrixPlotDemoData$heatmapData[[1]]
    exprData <- matrix(exprData[1, 1:50], nrow=1)
    plotBioMatrixHeatmap(exprData, maxValue=3, minValue=-3)