plotLocalMethylationProfile: Plot local methylation profile
In nrzabet/DMRcaller: Differentially Methylated Regions caller

Description Usage Arguments Value Author(s) Examples

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.

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

`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.

Invisibly returns NULL

Nicolae Radu Zabet

# 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")