plotBioMatrixCategoryData: Plot Category Data on caOmicsV bioMatrix Layout

In caOmicsV: Visualization of multi-dimentional cancer genomics data

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") 

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.