Show Signature Profile with Heatmap

Source: R/show_sig_profile_heatmap.R

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.

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'.

Value

a ggplot object.

Details

Support:

  • SBS-24

  • SBS-96

  • SBS-384

  • SBS-1536

  • SBS-6144

  • DBS-78

  • DBS-186

Examples

# \donttest{
# 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

# }