plotMethylationDataCoverage: Plot methylation data coverage

Description

This function plots the coverage for the bisulfite sequencing data.

Usage

plotMethylationDataCoverage(methylationData1, methylationData2 = NULL, breaks, regions = NULL, conditionsNames = NULL, context = "CG", proportion = TRUE, labels = NULL, col = NULL, pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5), contextPerRow = FALSE)

Arguments

methylationData1

the methylation data in condition 1 (see methylationDataList).

methylationData2

the methylation data in condition 2 (see methylationDataList). This is optional.

breaks

a numeric vector specifing the different values for the thresholds when computing the coverage.

regions

a GRanges object with the regions where to compute the coverage. If NULL, the coverage is computed genome-wide.

conditionsNames

a vector of character with the names of the conditions for methylationData1 and methylationData2.

context

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

proportion

a logical value indicating whether proportion or counts will be plotted.

labels

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

col

a character vector with the colors. It needs to contain a minimum of 2 colors per condition. If not or if NULL, the defalut colors will be used.

pch

the R symbols used to plot the data. It needs to contain a minimum of 2 symbols per condition. If not or if NULL, the defalut symbols will be used.

lty

the line types used to plot the data. It needs to contain a minimum of 2 line types per condition. If not or if NULL, the defalut line types will be used.

contextPerRow

a logical value indicating if the each row represents an individual context. If FALSE, each column will represent an individual context.

Value

Invisibly returns NULL

Details

This function plots the proportion of cytosines in a specific context that have at least a certain number of reads (x-axis)

Examples

Run this code

# load the methylation data
data(methylationDataList)

# plot the coverage in CG context
par(mar=c(4, 4, 3, 1)+0.1)
plotMethylationDataCoverage(methylationDataList[["WT"]],
                           methylationDataList[["met1-3"]],
                           breaks = c(1,5,10,15), regions = NULL,
                           conditionsNames = c("WT","met1-3"),
                           context = c("CG"), proportion = TRUE,
                           labels = LETTERS, col = NULL,
                           pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
                           contextPerRow = FALSE)

## Not run: 
# # plot the coverage in all three contexts
# plotMethylationDataCoverage(methylationDataList[["WT"]],
#                            methylationDataList[["met1-3"]],
#                            breaks = 1:15, regions = NULL,
#                            conditionsNames = c("WT","met1-3"),
#                            context = c("CG", "CHG", "CHH"),
#                            proportion = TRUE, labels = LETTERS, col = NULL,
#                            pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
#                            contextPerRow = FALSE)
# ## End(Not run)