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Last data update: 2014.03.03

R: Plot Legend on caOmicsV bioMatrix Layout

bioMatrixLegend

R Documentation

Plot Legend on caOmicsV bioMatrix Layout

Description

Draw legend including of heatmap color scale and data categories. Graphic device must be initialized first.

Usage

    bioMatrixLegend(heatmapNames=NULL, categoryNames=NULL, binaryNames=NULL, 
            heatmapMin=-3, heatmapMax=3, colorType="BlueWhiteRed")

Arguments

`heatmapNames`	character vector of length 2, name(s) of dataset for heatmap, e.g., "RNASeq" and/or "miRNASeq"
`categoryNames`	character vector of length 2 or more, names of categories, e.g., "Methylation High", "Methylation Low", ...
`binaryNames`	character vector of length 2 , names of binary data, e.g., "DNA Amplification" and "DNA Deletion".
`heatmapMin`	numeric, minimum values of heatmap plot data, default -3 (z-scores)
`heatmapMax`	numeric, maximum values of heatmap plot data, default 3 (z-scores)
`colorType`	characte veector, one of "BlueWhiteRed", "GreenWhiteRed", "GreenYellowRed", "GreenBlackRed" , or "YellowToRed"

Details

This function will plot legend on the bottom of matrix layout if any argument is defined. The order of legend items (from left to right) is heatmap color scale followed by colored boxes for category data legend then colored points for binary data legend.

Value

None

Author(s)

Henry Zhang

Examples

    data(biomatrixPlotDemoData)
    plotBioMatrix(biomatrixPlotDemoData, summaryType="text")
    bioMatrixLegend(heatmapNames=c("RNASeq", "miRNASeq"), 
        categoryNames=c("Methyl H", "Methyl L"), 
        binaryNames=c("CN LOSS", "CN Gain"),   
        colorType="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/bioMatrixLegend.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bioMatrixLegend
> ### Title: Plot Legend on caOmicsV bioMatrix Layout
> ### Aliases: bioMatrixLegend
> ### Keywords: methods
> 
> ### ** Examples
> 
>     data(biomatrixPlotDemoData)
>     plotBioMatrix(biomatrixPlotDemoData, summaryType="text")
>     bioMatrixLegend(heatmapNames=c("RNASeq", "miRNASeq"), 
+         categoryNames=c("Methyl H", "Methyl L"), 
+         binaryNames=c("CN LOSS", "CN Gain"),   
+         colorType="BlueWhiteRed")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>