sigminer (version 1.0.6)

show_sig_exposure: 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,
  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 exposure matrix with column representing samples (patients) and row representing signatures (row names must start with 'Sig').

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.

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

Examples

# NOT RUN {
# 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_M.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature exposure
p2 <- show_sig_exposure(sig)
p2
# }