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Last data update: 2014.03.03

R: Heatmap Plot on caOmicsV bioMatrix Layout

plotBioMatrixHeatmap

R Documentation

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(caOmicsV)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/caOmicsV/plotBioMatrixHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrixHeatmap
> ### Title: Heatmap Plot on caOmicsV bioMatrix Layout
> ### Aliases: plotBioMatrixHeatmap
> ### Keywords: methods
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>