R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plot Row Names on caOmicsV bioMatrix Layout

plotBioMatrixRowNames

R Documentation

Plot Row Names on caOmicsV bioMatrix Layout

Description

Plot row names on the left or right side of biomatrix plot area. Phenotype names, gene names, and remark notes are all plotted with this function. bioMatrix layout and graphic device must be initialized first.

Usage

    plotBioMatrixRowNames(geneNames, areaName, colors, side="left", 
            skipPlotRows=0, skipPlotColumns=0)

Arguments

`geneNames`	character vector, row names to be plotted
`areaName`	character vector, either "omicsData" or "phenotype"
`colors`	character vector of color names or R color specification
`side`	character vector, either "left" or "right"
`skipPlotRows`	non-negative integer, total rows on plot area that should be skipped from the first row, default 0
`skipPlotColumns`	non-negative integer, columns (sampleWidth) will be skipped when plotting items on remark area

Value

None

Author(s)

Henry Zhang

Examples

    initializeBioMatrixPlot(numOfGenes=20, numOfSamples=50)

    geneNames  <- paste0("gene_", 1:20)
    miRNANames <- paste0("miRNA_", 1:20)

    showBioMatrixPlotLayout(geneNames, paste("Sample", 1:50),  "Diagnosis")
    plotBioMatrixRowNames(miRNANames, areaName="omicsData", colors="blue", 
                side="right")

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/plotBioMatrixRowNames.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrixRowNames
> ### Title: Plot Row Names on caOmicsV bioMatrix Layout
> ### Aliases: plotBioMatrixRowNames
> ### Keywords: methods
> 
> ### ** Examples
> 
>     initializeBioMatrixPlot(numOfGenes=20, numOfSamples=50)
> 
>     geneNames  <- paste0("gene_", 1:20)
>     miRNANames <- paste0("miRNA_", 1:20)
> 
>     showBioMatrixPlotLayout(geneNames, paste("Sample", 1:50),  "Diagnosis")
>     plotBioMatrixRowNames(miRNANames, areaName="omicsData", colors="blue", 
+                 side="right")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>