Density Plot of \(\beta\)-Values

Source: R/scMethrix_plot.R

Density Plot of \(\beta\)-Values

plot_density(
  scm = NULL,
  assay = "score",
  regions = NULL,
  n_cpgs = 25000,
  pheno = NULL,
  col_palette = "RdYlGn",
  show_legend = TRUE,
  verbose = TRUE
)

Arguments

scm

scMethrix; the single cell methylation experiment
assay

string; name of an existing assay. Default = "score"
regions

Granges; genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a GenomicRanges object
n_cpgs

integer; Use these many random CpGs for plotting. Default 25000. Set it to NULL to use all - which can be memory expensive. The seed will be set to n_cpgs for consistency.
pheno

string; Col name of colData(m). Will be used as a factor to color different groups
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_density(scm = scMethrix_data)

#> Subsetting CpG sites...
#>    Subsetting by regions
#> Subset in 0.07s
#> Randomly selecting 25000 sites