oncoprintPlot: Function to plot genomic events in the style of...

Description Usage Arguments Value

View source: R/make.saturation.plots.r

Description

Function to plot genomic events in the style of oncoPrint/cBioPortal

Usage

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oncoprintPlot(
  summary.vec,
  snpmat.thisClus,
  amps.thisClus,
  dels.thisClus,
  fusions.thisClus,
  important.genes,
  band2gene,
  max.events,
  k
)

Arguments

summary.vec

: named vector of the counts, named 'Event name':'Type' where type is 'mut', 'amp', 'del', 'fus'. Mutations are in Entrez ID Amp/Deletion CNV events are in genomic band location

snpmat.thisClus

: SNP matrix subset to samples in current cluster

amps.thisClus

: CNV matrix subset to samples in current cluster (just amplifications)

dels.thisClus

: CNV matrix subset to samples in current cluster (just deletions)

fusions.thisClus

: Fusion matrix subset to samples in current cluster

important.genes

: well known genes to highlight in the analysis

band2gene

: mapping of genomic location IDs to gene name: vector of HUGO gene ids, named by genomic location

max.events

: maximum number of events to plot for the oncoplots

k

: current cluster number

Value

oncoprint event plot


MOMA documentation built on Nov. 8, 2020, 6:01 p.m.