ggFeatDens: create ggplot for density of starts of a GRanges in an...

In BiocOncoTK: Bioconductor components for general cancer genomics

Description

create ggplot for density of starts of a GRanges in an interval

Usage

ggFeatDens(
  gr,
  mcolvbl,
  chrname = "chr15",
  start = 20450000,
  end = 20730000,
  binwidth.in = 5000,
  basicfilt = function(data) dplyr::filter(data, Consequence ==
    "non_coding_transcript_exon_variant"),
  ylab.in = "feature\ndensity",
  slstyle = "UCSC"
)

Arguments

gr	GRanges instance of interest
mcolvbl	character(1) mcols(gr) has this variable that will be used to specify different groups for computing/colouring the density traces
chrname	character(1) chromosome/seqname
start	numeric(1) start of interval
end	numeric(1) end of interval
binwidth.in	numeric(1) for geom_freqpoly binwidth setting
basicfilt	a dplyr::filter operation, defaulting to select non-coding variants in mc3 MAF
ylab.in	character(1) label for y axis
slstyle	character(1) for GenomeInfoDb::seqlevelsStyle

Value

ggplot instance

Examples

ggFeatDens

BiocOncoTK documentation built on Nov. 8, 2020, 6:03 p.m.