A function to get the Red-Blue color scheme used by dChip

Description

A simple, vectorized function that computes a Red/Blue color for plotting microarray expression data.

Usage

GetColor(value, GreenRed=FALSE, DisplayRange=3)
dChip.colors(n)
greenred.colors(n)

Arguments

Details

GetColor is a simple mapping into RGB land provided by Cheng Li. dChip.colors provides functionality similar to that of topo.colors for the red–blue colors used for genome plots. greenred.colors does the same for the green-black-red gradient.

Value

A vector of RGB colors suitable for plotting in R.

Author(s)

R. Gentleman, based on an original by C. Li.

Examples

  set.seed(10)
  x <- rnorm(10)
  GetColor(x)
  dChip.colors(10)

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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> library(geneplotter)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geneplotter/GetColor.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GetColor
> ### Title: A function to get the Red-Blue color scheme used by dChip
> ### Aliases: GetColor dChip.colors greenred.colors
> ### Keywords: manip
> 
> ### ** Examples
> 
>   set.seed(10)
>   x <- rnorm(10)
>   GetColor(x)
 [1] "#FFFDFD" "#EFEFFF" "#8A8AFF" "#CCCCFF" "#FFE5E5" "#FFDDDD" "#9898FF"
 [8] "#E0E0FF" "#7474FF" "#E9E9FF"
>   dChip.colors(10)
 [1] "#0000FF" "#3333FF" "#6666FF" "#9999FF" "#CCCCFF" "#FFFFFF" "#FFCCCC"
 [8] "#FF9999" "#FF6666" "#FF3333" "#FF0000"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>