show_sig_exposure {sigminer}

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