DMRcaller (version 1.4.2)

plotMethylationProfile: Plot Methylation Profile

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

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)