plotBioMatrixHeatmap: Heatmap Plot on caOmicsV bioMatrix Layout

In caOmicsV: Visualization of multi-dimentional cancer genomics data

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

Author(s)

Henry Zhang

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)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: bc3net
Loading required package: c3net
Loading required package: infotheo
Loading required package: Matrix
Loading required package: lattice

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