Plot local methylation profile

Description

This function plots the methylation profile at one locus for the bisulfite sequencing data.The points on the graph represent methylation proportion of individual cytosines, their colour which sample they belong to and the intesity of the the colour how many reads that particular cytosine had. This means that darker colors indicate stronger evidence that the corresponding cytosine has the corresponding methylation proportion, while lighter colors indicate a weaker evidence. The solid lines represent the smoothed profiles and the intensity of the line the coverage at the corresponding position (darker colors indicate more reads while lighter ones less reads). The boxes on top represent the DMRs, where a filled box will represent a DMR which gained methylation while a box with a pattern represent a DMR that lost methylation. The DMRs need to have a metadafield "regionType" which can be either "gain" (where there is more methylation in condition 2 compared to condition 1) or "loss" (where there is less methylation in condition 2 compared to condition 1). In case this metadafield is missing all DMRs are drawn using a filled box. Finally, we also allow annotation of the DNA sequence. We represent by a black boxes all the exons, which are joined by a horizontal black line, thus, marking the full body of the gene. With grey boxes we mark the transposable elements. Both for genes and transposable elements we plot them over a mid line if they are on the positive strand and under the mid line if they are on the negative strand.

Usage

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plotLocalMethylationProfile(methylationData1, methylationData2, region,
  DMRs = NULL, conditionsNames = NULL, gff = NULL, windowSize = 150,
  context = "CG", labels = NULL, col = NULL, main = "",
  plotMeanLines = TRUE, plotPoints = TRUE)

Arguments

methylationData1

the methylation data in condition 1 (see methylationDataList).

methylationData2

the methylation data in condition 2 (see methylationDataList).

region

a GRanges object with the region where to plot the high resolution profile.

DMRs

a GRangesList object or a list with the list of DMRs (see computeDMRs or filterDMRs.

conditionsNames

the names of the two conditions. This will be used to plot the legend.

gff

a GRanges object with all elements usually imported from a GFF3 file. The gff file needs to have an metafield "type". Only the elements of type "gene", "exon" and "transposable_element" are plotted. Genes are represented as horizontal black lines, exons as a black rectangle and transposable elements as a grey rectangle. The elements are plotted on the corresponding strand (+ or -).

windowSize

the size of the triangle base used to smooth the average methylation profile.

context

the context in which the DMRs are computed ("CG", "CHG" or "CHH").

labels

a vector of character used to add a subfigure characters to the plot. If NULL nothing is added.

col

a character vector with the colors. It needs to contain a minimum of 4 length(DMRs) colors. If not or if NULL, the defalut colors will be used.

main

a character with the title of the plot

plotMeanLines

a logical value indicating whether to plot the mean lines or not.

plotPoints

a logical value indicating whether to plot the points or not.

Value

Invisibly returns NULL

Author(s)

Nicolae Radu Zabet

Examples

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# load the methylation data
data(methylationDataList)
# load the gene annotation data
data(GEs)

#select the genes
genes <- GEs[which(GEs$type == "gene")]

# the coordinates of the area to be plotted
chr3Reg <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(510000,530000))

# load the DMRs in CG context
data(DMRsNoiseFilterCG)

DMRsCGlist <- list("noise filter"=DMRsNoiseFilterCG)


# plot the CG methylation
par(mar=c(4, 4, 3, 1)+0.1)
par(mfrow=c(1,1))
plotLocalMethylationProfile(methylationDataList[["WT"]],
                           methylationDataList[["met1-3"]], chr3Reg,
                           DMRsCGlist, c("WT", "met1-3"), GEs,
                           windowSize=100, main="CG methylation")