plot_coverage: Coverage QC Plots

In methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Description

Coverage QC Plots

Usage

plot_coverage(
  m,
  type = c("hist", "dens"),
  pheno = NULL,
  perGroup = FALSE,
  lim = 100,
  size.lim = 1e+06,
  col_palette = "RdYlGn"
)

Arguments

m	Input methrix object
type	Choose between 'hist' (histogram) or 'dens' (density plot).
pheno	Column name of colData(m). Will be used as a factor to color different groups in the plot.
perGroup	Color the plots in a sample-wise manner?
lim	Maximum coverage value to be plotted.
size.lim	The maximum number of observarions (sites*samples) to use. If the dataset is larger that this, random sites will be selected from the genome.
col_palette	Name of the RColorBrewer palette to use for plotting.

Value

ggplot2 object

Examples

data('methrix_data')
plot_coverage(m = methrix_data)

methrix documentation built on Feb. 13, 2021, 2 a.m.