plotGene: Plot genes using ggbio::geom_alignment

In oncogenetics/oncofunco: Custom function for Oncogenetics team

Plot genes using ggbio::geom_alignment

Description

This function returns GRanges object, used as input for plotting gene track Warning: too much dependency to other packages, will need to rewrite/update the code in future far far away... Warning: only works for LE at the moment with pre-loaded bio packages

Usage

plotGene(
  chrom = NULL,
  chromStart = NULL,
  chromEnd = NULL,
  hits = NULL,
  vline = NULL,
  pad = TRUE
)

Arguments

chrom	chromosome name, must be character class with length(chrom)==1, e.g.: chr1"
chromStart, chromEnd	Region range, zoom, minimum BP and maximum BP, advised to keep this less than 5Mb.
hits	Default NULL. Color genes based on strand and hits.
vline	Mark hits on genes
pad	Default is TRUE, to align plots pad strings with spaces, using oncofunco::strPadLeft().

Value

a list with 2 objects: $genePlot ggplot object and $geneCount numeric

Author(s)

Tokhir Dadaev

oncogenetics/oncofunco documentation built on March 9, 2024, 5:23 p.m.