show_cn_components: Show Copy Number Components

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

Show Copy Number Components

Description

Show classified components ("Wang" ("W") method) for copy number data.

Usage

show_cn_components(
  parameters,
  method = "Wang",
  show_weights = TRUE,
  log_y = FALSE,
  return_plotlist = FALSE,
  base_size = 12,
  nrow = 2,
  align = "hv",
  ...
)

Arguments

parameters	a data.frame contain parameter components, obtain this from sig_tally function.
method	method for feature classification, can be one of "Wang" ("W"), "S" (for method described in Steele et al. 2019), "X" (for method described in Tao et al. 2023).
show_weights	default is TRUE, show weights for each component. Only used when method is "Macintyre".
log_y	logical, if TRUE, show log10 based y axis, only works for input from "Wang" ("W") method.
return_plotlist	if TRUE, return a list of ggplot objects but a combined plot.
base_size	overall font size.
nrow	(optional) Number of rows in the plot grid.
align	(optional) Specifies whether graphs in the grid should be horizontally ("h") or vertically ("v") aligned. Options are "none" (default), "hv" (align in both directions), "h", and "v".
...	other options pass to plot_grid function of cowplot package.

Value

a ggplot object

Author(s)

Shixiang Wang [e-mail]

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