show_sig_exposure: Plot Signature Exposure

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

Plot Signature Exposure

Description

Currently support copy number signatures and mutational signatures.

Usage

show_sig_exposure(
  Signature,
  sig_names = NULL,
  groups = NULL,
  grp_order = NULL,
  grp_size = NULL,
  samps = NULL,
  cutoff = NULL,
  style = c("default", "cosmic"),
  palette = use_color_style(style),
  base_size = 12,
  font_scale = 1,
  rm_space = FALSE,
  rm_grid_line = TRUE,
  rm_panel_border = FALSE,
  hide_samps = TRUE,
  legend_position = "top"
)

Arguments

Signature	a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw absolute exposure matrix with column representing samples (patients) and row representing signatures (signature names must end with different digital numbers, e.g. Sig1, Sig10, x12). If you named signatures with letters, you can specify them by sig_names parameter.
sig_names	set name of signatures, can be a character vector.
groups	sample groups, default is NULL.
grp_order	order of groups, default is NULL.
grp_size	font size of groups.
samps	sample vector to filter samples or sort samples, default is NULL.
cutoff	a cutoff value to remove hyper-mutated samples.
style	plot style, one of 'default' and 'cosmic', works when parameter set_gradient_color is FALSE.
palette	palette used to plot, default use a built-in palette according to parameter style.
base_size	overall font size.
font_scale	a number used to set font scale.
rm_space	default is FALSE. If TRUE, it will remove border color and expand the bar width to 1. This is useful when the sample size is big.
rm_grid_line	default is FALSE, if TRUE, remove grid lines of plot.
rm_panel_border	default is TRUE for style 'cosmic', remove panel border to keep plot tight.
hide_samps	if TRUE, hide sample names.
legend_position	position of legend, default is 'top'.

Value

a ggplot object

Author(s)

Shixiang Wang

Examples

# Load mutational signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature exposure
p1 <- show_sig_exposure(sig2)
p1

# Load copy number signature
load(system.file("extdata", "toy_copynumber_signature_by_W.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature exposure
p2 <- show_sig_exposure(sig)
p2

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