plotMethylationProfile {DMRcaller} | R Documentation |
This function plots the low resolution profiles for the bisulfite sequencing data.
plotMethylationProfile(methylationProfiles, autoscale = FALSE, labels = NULL, title = "", col = NULL, pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5))
methylationProfiles |
a |
autoscale |
a |
labels |
a |
title |
the plot title. |
col |
a |
pch |
the R symbols used to plot the data. |
lty |
the line types used to plot the data. |
Invisibly returns NULL
Nicolae Radu Zabet
plotMethylationProfileFromData
,
computeMethylationProfile
and methylationDataList
# load the methylation data data(methylationDataList) # the region where to compute the profile region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6)) # compute low resolution profile in 20 Kb windows lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]], region, windowSize = 20000, context = "CG") lowResProfilsCG <- GRangesList("WT" = lowResProfileWTCG) #plot the low resolution profile par(mar=c(4, 4, 3, 1)+0.1) par(mfrow=c(1,1)) plotMethylationProfile(lowResProfilsCG, autoscale = FALSE, title="CG methylation on Chromosome 3", col=c("#D55E00","#E69F00"), pch = c(1,0), lty = c(4,1)) ## Not run: # compute low resolution profile in 10 Kb windows in CG context lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]], region, windowSize = 10000, context = "CG") lowResProfileMet13CG <- computeMethylationProfile( methylationDataList[["met1-3"]], region, windowSize = 10000, context = "CG") lowResProfileCG <- GRangesList("WT" = lowResProfileWTCG, "met1-3" = lowResProfileMet13CG) # compute low resolution profile in 10 Kb windows in CHG context lowResProfileWTCHG <- computeMethylationProfile(methylationDataList[["WT"]], region, windowSize = 10000, context = "CHG") lowResProfileMet13CHG <- computeMethylationProfile( methylationDataList[["met1-3"]], region, windowSize = 10000, context = "CHG") lowResProfileCHG <- GRangesList("WT" = lowResProfileWTCHG, "met1-3" = lowResProfileMet13CHG) # plot the low resolution profile par(mar=c(4, 4, 3, 1)+0.1) par(mfrow=c(2,1)) plotMethylationProfile(lowResProfileCG, autoscale = FALSE, labels = LETTERS[1], title="CG methylation on Chromosome 3", col=c("#D55E00","#E69F00"), pch = c(1,0), lty = c(4,1)) plotMethylationProfile(lowResProfileCHG, autoscale = FALSE, labels = LETTERS[2], title="CHG methylation on Chromosome 3", col=c("#0072B2", "#56B4E9"), pch = c(16,2), lty = c(3,2)) ## End(Not run)