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Last data update: 2014.03.03

R: Binary Data Plot on caOmicsV bioMatrix Layout

plotBioMatrixBinaryData

R Documentation

Binary Data Plot on caOmicsV bioMatrix Layout

Description

Plot binary data as points in the inside of each rectangle(sample). This function plot all rows on omics data area and only the positive samples will be shown with colored points. For one row plot, pass data as vector and supply correct skipPlotRow parameter to define where to plot. bioMatrix layout and graphic device must be initialized first.

Usage

    plotBioMatrixBinaryData(binaryData, areaName="omicsData", scatterType=19, 
        scatterSize=1, totalSubRow=1, subRowIndex=1, sampleColor="black", 
        skipPlotRow=0)

Arguments

`binaryData`	vector or matrix with values of 0 and 1 only
`areaName`	character vector, either "omicsData" or "phenotype"
`scatterType`	non-negative integer, same as pch, default 19
`scatterSize`	non-negative numeric, same as cex
`totalSubRow`	non-negative integer, how many sub-rows in a sample area
`subRowIndex`	non-negative integer, which subrow will be plotted
`sampleColor`	character vector for color name(s) or R color specification
`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")

    binaryData <- matrix(c(rep(1, 15), rep(0, 20), rep(1, 15)), nrow=1)
    plotBioMatrixBinaryData(binaryData, scatterType=16)

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.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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'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/plotBioMatrixBinaryData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrixBinaryData
> ### Title: Binary Data Plot on caOmicsV bioMatrix Layout
> ### Aliases: plotBioMatrixBinaryData
> ### Keywords: methods
> 
> ### ** Examples
> 
>     initializeBioMatrixPlot(numOfGenes=1, numOfSamples=50)
>     showBioMatrixPlotLayout("Gene", paste("Sample", 1:50),  "Diagnosis")
> 
>     binaryData <- matrix(c(rep(1, 15), rep(0, 20), rep(1, 15)), nrow=1)
>     plotBioMatrixBinaryData(binaryData, scatterType=16) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>