show_catalogue: Show Alteration Catalogue Profile

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Show Alteration Catalogue Profile

Description

Show Alteration Catalogue Profile

Usage

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

data("simulated_catalogs")
p <- show_catalogue(simulated_catalogs$set1, style = "cosmic")
p

sigminer documentation built on May 29, 2024, 3:11 a.m.