character; a color, the lower limit of the color palette
col2
character; a color, the mid point of the color palette
col3
character; a color, the upper limit of the color palette
Details
A bidimensional color palette is built. First a set1 of round(n/2)
colors ranging from col1 and col2 is defined.
Then a set2 of round(n/2) colors ranging from col2 and col3 is
defined. Set1 and set2 are concatenated, as the first row of a k X n
matrix M. Finally, for each column i of M, k colors ranging from white
to M[1,i] are defined.
It is used in the GRheatmapPlot function to have a color palette
simultaneously representing the intensity of an event (n) and its
significance (k). See the example.
res <- palette2d(50, 10)
plot(rep(1:ncol(res),each=nrow(res)), rep(1:nrow(res),times=ncol(res)), col=res,
pch=20, xlab='intensity', ylab='significance')
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(compEpiTools)
Loading required package: topGO
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
Loading required package: graph
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GO.db
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: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/compEpiTools/palette2d.Rd_%03d_medium.png", width=480, height=480)
> ### Name: palette2d
> ### Title: build a two dimensional color palette
> ### Aliases: palette2d
>
> ### ** Examples
>
> res <- palette2d(50, 10)
> plot(rep(1:ncol(res),each=nrow(res)), rep(1:nrow(res),times=ncol(res)), col=res,
+ pch=20, xlab='intensity', ylab='significance')
>
>
>
>
>
> dev.off()
null device
1
>