colors: Create set of colors, interpolating through a set of...

In oligo: Preprocessing tools for oligonucleotide arrays

Description

Create set of colors, interpolating through a set of preferred colors.

Usage

darkColors(n)
seqColors(n)
seqColors2(n)
divColors(n)

Arguments

n	integer determining number of colors to be generated

Details

darkColors is based on the Dark2 palette in RColorBrewer, therefore useful to describe qualitative features of the data.

seqColors is based on Blues and generates a gradient of blues, therefore useful to describe quantitative features of the data. seqColors2 behaves similarly, but it is based on OrRd (white-orange-red).

divColors is based on the RdBu pallete in RColorBrewer, therefore useful to describe quantitative features ranging on two extremes.

Examples

x <- 1:10
y <- 1:10
cols1 <- darkColors(10)
cols2 <- seqColors(10)
cols3 <- divColors(10)
cols4 <- seqColors2(10)
plot(x, y, col=cols1, xlim=c(1, 13), pch=19, cex=3)
points(x+1, y, col=cols2, pch=19, cex=3)
points(x+2, y, col=cols3, pch=19, cex=3)
points(x+3, y, col=cols4, pch=19, cex=3)
abline(0, 1, lty=2)
abline(-1, 1, lty=2)
abline(-2, 1, lty=2)
abline(-3, 1, lty=2)

Example output

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

Loading required package: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
Warning messages:
1: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
2: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind' 
3: In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
4: multiple methods tables found for 'dims' 

oligo documentation built on Nov. 8, 2020, 6:52 p.m.