ggFeatDens {BiocOncoTK}R Documentation

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

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

[Package BiocOncoTK version 1.4.0 Index]