Coverage QC Plots

Source: R/scMethrix_plot.R

Coverage QC Plots

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)

#> Randomly selecting 25000 sites