plotMethylationProfile: Plot Methylation Profile

In nrzabet/DMRcaller: Differentially Methylated Regions caller

Description

This function plots the low resolution profiles for the bisulfite sequencing data.

Usage

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))

Arguments

methylationProfiles	a GRangesList object. Each GRanges object in the list is generated by calling the function computeMethylationProfile.
autoscale	a logical value indicating whether the values are autoscalled for each context or not.
labels	a vector of character used to add a subfigure characters to the plot. If NULL nothing is added.
title	the plot title.
col	a character vector with the colours. It needs to contain a minimum of 2 colours per context. If not or if NULL, the defalut colours will be used.
pch	the R symbols used to plot the data.
lty	the line types used to plot the data.

Value

Invisibly returns NULL

Author(s)

Nicolae Radu Zabet

See Also

plotMethylationProfileFromData, computeMethylationProfile and methylationDataList

Examples

# 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)

nrzabet/DMRcaller documentation built on May 23, 2019, 2:50 p.m.