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Last data update: 2014.03.03

R: Plot Sample Data on caOmicsV bioMatrix Layout

plotBioMatrixSampleData

R Documentation

Plot Sample Data on caOmicsV bioMatrix Layout

Description

Plot colored polygons on phenotype area of caOmicsV bioMatrix layout to show sample information such as diagnosis, tissue type, ... bioMatrix layout and graphic device must be initialized first.

Usage

    plotBioMatrixSampleData(rowNumber, areaName, fillColor=NA, 
        borderColor=NA, topAdjust=0, bottomAdjust=0)

Arguments

`rowNumber`	non-negative integer, number of the row where the data to be plotted
`areaName`	character vector, either "phenotype" or "omicsdata"
`fillColor`	character vector of color names or vector of R color specification
`borderColor`	character vector or a R colors specification for boarder color
`topAdjust`	non-negative numeric, height that will be reduced from top
`bottomAdjust`	non-negative numeric, height that will be reduced from bottom

Value

None

Author(s)

Henry Zhang

Examples

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

    sampleColor <- c(rep("blue", 25), rep("red", 25))
    plotBioMatrixSampleData(rowNumber=1, sampleColor, areaName="phenotype")

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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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/plotBioMatrixSampleData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrixSampleData
> ### Title: Plot Sample Data on caOmicsV bioMatrix Layout
> ### Aliases: plotBioMatrixSampleData
> ### Keywords: methods
> 
> ### ** Examples
> 
>     initializeBioMatrixPlot(numOfGenes=1, numOfSamples=50)
>     showBioMatrixPlotLayout("Gene", paste("Sample", 1:50),  "Diagnosis")
> 
>     sampleColor <- c(rep("blue", 25), rep("red", 25))
>     plotBioMatrixSampleData(rowNumber=1, sampleColor, areaName="phenotype") 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>