plotEmpiricalDistribution {dmrseq} | R Documentation

## Plot the empirical distribution of the methylation beta vals or coverage

### Description

Uses ggplot2 to plot smoothed density histograms of methylation proportions (beta values), or coverage. Methylation proportion densities are weighted by coverage. The number of curves plotted will be equal to the number of different values of `testCovariate`, unless `bySample` is TRUE. This can take quite some time to execute for a large object, so it is recommended to first take a random sample of loci (say one million) before plotting.

### Usage

    plotEmpiricalDistribution(bs, testCovariate = NULL, bySample = FALSE,
      type = "M", adj = 2.5)

### Arguments

`bs` | a BSseq object
`testCovariate` | character specifying the column name of the `pData` slot of the BSseq object to include in the plot legend.
`bySample` | logical whether to plot a separate line for each sample, even if the grouping `testCovariate` is specified. Default value is FALSE (so samples with the same value of `testCovariate` will be collapsed into the same line). If `testCovariate` is not specified, this parameter does not have an effect and samples are automatically plotted separately.
`type` | a character indicating which type of density to plot - the methylation (beta) values ("M") or the coverage ("Cov"). Default is "M".
`adj` | a numeric value for the `adjust` parameter to pass to the `geom_line` function. Specifies how smooth the make the function.

### Value

a ggplot object

### Examples

    data(BS.chr21)

    # plot beta values by sample group
    plotEmpiricalDistribution(BS.chr21, testCovariate="CellType")

[Package dmrseq version 1.6.0 Index]