Show Alteration Catalogue Profile

show_catalogue(
  catalogue,
  mode = c("SBS", "copynumber", "DBS", "ID", "RS"),
  method = "Wang",
  normalize = c("raw", "row", "feature"),
  style = c("default", "cosmic"),
  samples = NULL,
  samples_name = NULL,
  x_lab = "Components",
  y_lab = "Counts",
  ...
)

Arguments

catalogue: result from sig_tally or a matrix with row representing components (motifs) and column representing samples
mode: signature type for plotting, now supports 'copynumber', 'SBS', 'DBS', 'ID' and 'RS' (genome rearrangement signature).
method: method for copy number feature classification in sig_tally, can be one of "Wang" ("W"), "S".
normalize: normalize method.
style: plot style, one of 'default' and 'cosmic'.
samples: default is NULL, show sum of all samples in one row. If not NULL, show specified samples.
samples_name: set the sample names shown in plot.
x_lab: x axis lab.
y_lab: y axis lab.
...: other arguments passing to show_sig_profile.

Value

a ggplot object

Examples

# \donttest{
data("simulated_catalogs")
p <- show_catalogue(simulated_catalogs$set1, style = "cosmic")
p

# }