plot_coverage: Coverage QC Plots

In CompEpigen/scMethrix: Fast and efficient summarization of single cell whole genome bisulfate data

Description

Coverage QC Plots

Usage

plot_coverage(
  scm = NULL,
  type = c("histogram", "density"),
  pheno = NULL,
  max_cov = 100,
  obs_lim = 1e+06,
  col_palette = "RdYlGn",
  show_legend = TRUE,
  verbose = TRUE
)

Arguments

scm	scMethrix; the single cell methylation experiment
type	string; Choose between 'histogram' (histogram) or 'density' (density plot).
pheno	string; Col name of colData(m). Will be used as a factor to color different groups
max_cov	integer; Maximum coverage value to be plotted.
obs_lim	integer; The maximum number of observations (sites*samples) to use. If the dataset is larger that this, random sites will be selected from the genome.
col_palette	string; Name of the RColorBrewer palette to use for plotting.
show_legend	boolean; Display the legend on the plot
verbose	boolean; Flag for outputting function status messages. Default = TRUE

Value

ggplot2 object

Examples

data('scMethrix_data')
plot_coverage(scm = scMethrix_data)

CompEpigen/scMethrix documentation built on Nov. 6, 2021, 3:09 p.m.