show_sig_profile_heatmap: Show Signature Profile with Heatmap

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

Show Signature Profile with Heatmap

Description

This is a complementary function to show_sig_profile(), it is used for visualizing some big signatures, i.e. SBS-1536, not all signatures are supported. See details for current supported signatures.

Usage

show_sig_profile_heatmap(
  Signature,
  mode = c("SBS", "DBS"),
  normalize = c("row", "column", "raw"),
  filters = NULL,
  x_lab = NULL,
  y_lab = NULL,
  legend_name = "auto",
  palette = "red",
  x_label_angle = 90,
  x_label_vjust = 1,
  x_label_hjust = 0.5,
  y_label_angle = 0,
  y_label_vjust = 0.5,
  y_label_hjust = 1,
  flip_xy = FALSE,
  sig_names = NULL,
  sig_orders = NULL,
  check_sig_names = TRUE
)

Arguments

Signature	a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix with row representing components (motifs) and column representing signatures (column names must start with 'Sig').
mode	one of "SBS" and "DBS".
normalize	one of 'row', 'column', 'raw' and "feature", for row normalization (signature), column normalization (component), raw data, row normalization by feature, respectively. Of note, 'feature' only works when the mode is 'copynumber'.
filters	a pattern used to select components to plot.
x_lab	x label.
y_lab	y label.
legend_name	name of figure legend.
palette	color for value.
x_label_angle	angle for x axis text.
x_label_vjust	vjust for x axis text.
x_label_hjust	hjust for x axis text.
y_label_angle	angle for y axis text.
y_label_vjust	vjust for y axis text.
y_label_hjust	hjust for y axis text.
flip_xy	if TRUE, flip x axis and y axis.
sig_names	subset signatures or set name of signatures, can be a character vector. Default is NULL, prefix 'Sig' plus number is used.
sig_orders	set order of signatures, can be a character vector. Default is NULL, the signatures are ordered by alphabetical order. If an integer vector set, only specified signatures are plotted.
check_sig_names	if TRUE, check signature names when input is a matrix, i.e., all signatures (colnames) must start with 'Sig'.

Details

Support:

• SBS-24

• SBS-96

• SBS-384

• SBS-1536

• SBS-6144

• DBS-78

• DBS-186

Value

a ggplot object.

Examples

# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Show signature profile
p1 <- show_sig_profile_heatmap(sig2, mode = "SBS")
p1

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