sigminer (version 1.0.6)

show_catalogue: Show Alteration Catalogue Profile

Description

Show Alteration Catalogue Profile

Usage

show_catalogue(
  catalogue,
  mode = c("SBS", "copynumber", "DBS", "ID"),
  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' and 'ID'.

method

method for copy number feature classfication in sig_tally, can be one of "Macintyre" ("M") and "Wang" ("W").

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

# NOT RUN {
load(system.file("extdata", "toy_copynumber_tally_M.RData",
  package = "sigminer", mustWork = TRUE
))
p <- show_catalogue(cn_tally_M,
  mode = "copynumber", method = "M",
  style = "cosmic", paint_axis_text = FALSE
)
p
# }