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

In geneplotter: Graphics related functions for Bioconductor

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

value	The vector of expression values.
GreenRed	If TRUE the Green-Red colors are produced, otherwise Red-Blue are procduced.
DisplayRange	A parameter controlling the range of value's that will be plotted.
n	An integer saying how many colors to be in the palette.

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)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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 object is masked from 'package:base':

    expand.grid

Loading required package: XML
 [1] "#FFFDFD" "#EFEFFF" "#8A8AFF" "#CCCCFF" "#FFE5E5" "#FFDDDD" "#9898FF"
 [8] "#E0E0FF" "#7474FF" "#E9E9FF"
 [1] "#0000FF" "#3333FF" "#6666FF" "#9999FF" "#CCCCFF" "#FFFFFF" "#FFCCCC"
 [8] "#FF9999" "#FF6666" "#FF3333" "#FF0000"

geneplotter documentation built on Nov. 8, 2020, 7:13 p.m.