plotEvents: Plot barchart of genomic events

Description Usage Arguments Value

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

Description

Plot barchart of genomic events

Usage

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plotEvents(
  summary.vec,
  highlight.genes = NULL,
  genomeBand_2_gene = NULL,
  samples.total,
  max.muts = 10,
  max.cnv = 5
)

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

highlight.genes

: well known genes to highlight in the analysis in

genomeBand_2_gene

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

samples.total

: number of samples in the subtype, used to calculate percentages

max.muts

: maximum number of mutations to get per sample, default is 10

max.cnv

: maximum number of cnvs to per sample, default is 5

Value

plot object


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