R: Plot methylation profile from data

plotMethylationProfileFromData {DMRcaller}

R Documentation

Plot methylation profile from data

Description

This function plots the low resolution profiles for all bisulfite sequencing data.

Usage

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

Arguments

`methylationData1`	the methylation data in condition 1 (see `methylationDataList`).
`methylationData2`	the methylation data in condition 2 (see `methylationDataList`). This is optional.
`regions`	a `GRanges` object with the regions where to plot the profiles.
`conditionsNames`	the names of the two conditions. This will be used to plot the legend.
`context`	a `vector` with all contexts in which the DMRs are computed (`"CG"`, `"CHG"` or `"CHH"`).
`windowSize`	a `numeric` value indicating the size of the window in which methylation is averaged.
`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 character to the plot. If `NULL` nothing is added.
`col`	a `character` vector with the colours. It needs to contain a minimum of 2 colours per condition. If not or if `NULL`, the defalut colours 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

Author(s)

Nicolae Radu Zabet

Examples

# load the methylation data
data(methylationDataList)

#plot the low resolution profile at 10 Kb resolution
par(mar=c(4, 4, 3, 1)+0.1)
plotMethylationProfileFromData(methylationDataList[["WT"]],
                               methylationDataList[["met1-3"]],
                               conditionsNames=c("WT", "met1-3"),
                               windowSize = 20000, autoscale = TRUE,
                               context = c("CHG"))

## Not run: 
#plot the low resolution profile at 5 Kb resolution
par(mar=c(4, 4, 3, 1)+0.1)
plotMethylationProfileFromData(methylationDataList[["WT"]],
                               methylationDataList[["met1-3"]],
                               conditionsNames=c("WT", "met1-3"),
                               windowSize = 5000, autoscale = TRUE,
                               context = c("CG", "CHG", "CHH"),
                               labels = LETTERS)

## End(Not run)

[Package DMRcaller version 1.18.0 Index]