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Last data update: 2014.03.03

R: Default Plot Method for caOmicsV bioMatrix Layout Plot

plotBioMatrix

R Documentation

Default Plot Method for caOmicsV bioMatrix Layout Plot

Description

A sample way to plot sample information and genomic data with default settings.

Usage

    plotBioMatrix(dataSet, summaryType=c("text", "bar"), summarybyRow=TRUE, 
        heatmapMax=NULL, heatmapMin=NULL, heatmapColor="BlueWhiteRed")

Arguments

`dataSet`	an object, returned from method of getPlotDataSet(), with all plot data
`summaryType`	character vector, either "text" or "bar", for plot type of summary data
`summarybyRow`	logic, if the summary data is for each row or for each column
`heatmapMax`	numeric, maximum value for heatmap plot, set to NULL to use the maximum value in input data.
`heatmapMin`	numeric, minimum value for heatmap plot, set to NULL to use the minimum value in input data.
`heatmapColor`	character vector,one of "BlueWhiteRed", "GreenWhiteRed", "GreenYellowRed", "GreenBlackRed" , or "YellowToRed"

Value

None

Author(s)

Henry Zhang

Examples

    data(biomatrixPlotDemoData)
    plotBioMatrix(biomatrixPlotDemoData, summaryType="text", 
        summarybyRow=TRUE, heatmapMax=3, heatmapMin=-3, 
        heatmapColor="BlueWhiteRed")

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/plotBioMatrix.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBioMatrix
> ### Title: Default Plot Method for caOmicsV bioMatrix Layout Plot
> ### Aliases: plotBioMatrix
> ### Keywords: methods
> 
> ### ** Examples
> 
>     data(biomatrixPlotDemoData)
>     plotBioMatrix(biomatrixPlotDemoData, summaryType="text", 
+         summarybyRow=TRUE, heatmapMax=3, heatmapMin=-3, 
+         heatmapColor="BlueWhiteRed") 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>