oncoprint: oncoprint

In mskilab/skitools: Various mskilab R utilties

oncoprint

Description

Simple wrapper around to oncoPrint from complexHeatmap package to allow quick plotting of patients x genes + metadata. Uses the data gathered by oncotab to generate quick simple plots that include a core matrix of genes x patients containing data on SCNA, (complex), fusions, SNV, and indels. Additional tracks plotting log TMB + 1, log SV burden, complex events, SNV signatures can be provided.

Usage

oncoprint(
  tumors = NULL,
  oncotab = NULL,
  genes = c("KRAS", "EGFR", "BRAF", "TP53", "TERT", "CCND1", "MYC", "PIK3CA", "PTEN",
    "CDKN2A", "ARID1A", "SMARCA4"),
  split = NULL,
  sort = TRUE,
  sort.genes = sort,
  sort.tumors = sort,
  columns = NULL,
  noncoding = FALSE,
  cna = TRUE,
  tmb = TRUE,
  pp = TRUE,
  signature = TRUE,
  svevents = TRUE,
  basic = FALSE,
  ppdf = TRUE,
  return.oncotab = FALSE,
  return.mat = FALSE,
  wes = TRUE,
  drop = TRUE,
  drop.genes = FALSE,
  track.height = 1,
  signature.thresh = 0.2,
  signature.main = c(1:5, 7, 9, 13),
  outframe.fusions = FALSE,
  track.gap = track.height/2,
  split.gap = 1,
  colnames.fontsize = 10,
  rownames.fontsize = 10,
  track.fontsize = 10,
  mc.cores = 1,
  verbose = FALSE,
  height = 20,
  width = 20,
  ...
)

Arguments

tumors	keyed table of tumors (aka pairs table) with field $oncotable which points to a cached .rds file of an oncotable e.g. produced by oncotable function or Oncotable module / task
oncotab	output from oncotable function with field $id
genes	character vector of genes
split	character of name of column in tumors table to split on (NULL)
sort	logical flag whether to automatically sort rows i.e. genes and columns i.e. tumors in a "stair step" pattern or default to the provided (TRUE)
sort.genes	logical flag whether to sort rows i.e. genes with respect to their frequency (TRUE)
sort.tumors	logical flag whether to sort columns i.e. patients in a stairstep pattern with respect to the provided gene order (TRUE)
columns	additional columns of tumors matrix to plot as horizontal tracks below the main track
noncoding	logical flag whether to show non protein coding mutations
tmb	logical flag whether to show TMB bar plot (TRUE)
pp	logical flag whether to show purity / ploidy (if data is provided / available) (TRUE)
svevents	logical flag whether to show events (if data is provided / available) (TRUE)
ppdf	whether to print to pdf via ppdf
return.mat	whether to return.mat
wes	logical flag whether to use wesanderson coolors
track.height	height of tracks in 'cm'
signature.thresh	lower threshold for non main signature fraction in at least one sample to plot
signature.main	integer indices of main COSMIC signatures to keep
outframe.fusions	show fusions that are out-of-frame (FALSE)
split.gap	gap between splits
mc.cores	multicore threads to use for $oncotable loading from tumors table (not relevant if oncotab provided)
...	other arguments to ppdf
sv.stack	logical flag whether to stack bar plot simple and complex SV event counts (FALSE)
signatures	logical flag whether to show signatures (if data is provided / available) (TRUE)
tmb.log	logical flag whether to log TMB + 1 (TRUE)
cex	length 1 or 2 vector canvas expansion factor to apply to the oncoprint itself (relative to 10 x 10 cm) (c(1,3))

Value

ComplexHeatmap object (if ppdf = FALSE), and genotype matrix (if return)

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.