plotMethylationDataCoverage: Plot methylation data coverage
In nrzabet/DMRcaller: Differentially Methylated Regions caller

Description Usage Arguments Details Value Author(s) See Also Examples

This function plots the coverage for the bisulfite sequencing data.

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)

`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.

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

Invisibly returns NULL

Nicolae Radu Zabet

computeMethylationDataCoverage, methylationDataList

# 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)