show_cn_features: Show Copy Number Feature Distributions

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

Show Copy Number Feature Distributions

Description

Show Copy Number Feature Distributions

Usage

show_cn_features(
  features,
  method = "Wang",
  rm_outlier = FALSE,
  ylab = NULL,
  log_y = FALSE,
  return_plotlist = FALSE,
  base_size = 12,
  nrow = 2,
  align = "hv",
  ...
)

Arguments

features	a feature list generate 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).
rm_outlier	default is FALSE, if TRUE, remove outliers. Only works when method is "Wang" ("W").
ylab	lab of y axis.
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

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