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Last data update: 2014.03.03

R: Plot Category Data on caOmicsV bioMatrix Layout

plotBioMatrixCategoryData

R Documentation

Plot Category Data on caOmicsV bioMatrix Layout

Description

Draw rectangle outline for one or more row(s) of samples to represent categorical values. This function highlights all samples on each row. bioMatrix layout and graphic device must be initialized first.

Usage

    plotBioMatrixCategoryData(categoryData, 
            areaName=c("omicsData", "phenotype"), 
            sampleColors=palette(), 
            lineWidth=1, skipPlotRow=0)

Arguments

`categoryData`	vector or matrix of categorical values, such as 'High', 'low', and 'No'
`areaName`	character vector, either "omicsdata" or "phenotype"
`sampleColors`	character vector for color names or vector of R color specification
`lineWidth`	non-negative integer, graphic parameter for lwd (line width), default 1
`skipPlotRow`	non-negative integer, total rows on plot area that should be skipped when only one row to plot, default 0.

Value

None

Author(s)

Henry Zhang

Examples

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

    categoryData <- matrix(c(rep(1, 15), rep(0, 20), rep(1, 15)), nrow=1)
    plotBioMatrixCategoryData(categoryData, areaName="omicsData")

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)

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> 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/plotBioMatrixCategoryData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrixCategoryData
> ### Title: Plot Category Data on caOmicsV bioMatrix Layout
> ### Aliases: plotBioMatrixCategoryData
> ### Keywords: methods
> 
> ### ** Examples
> 
>     initializeBioMatrixPlot(numOfGenes=1, numOfSamples=50)
>     showBioMatrixPlotLayout("Gene", paste("Sample", 1:50),  "Diagnosis")
> 
>     categoryData <- matrix(c(rep(1, 15), rep(0, 20), rep(1, 15)), nrow=1)
>     plotBioMatrixCategoryData(categoryData, areaName="omicsData") 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>