plotEnsGenes: Plot ENSEMBL genes
In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

plotEnsGenes

R Documentation

Plot ENSEMBL genes

Description

Plot ENSEMBL genes in region

Usage

plotEnsGenes(
  ensdb,
  minRange,
  maxRange,
  chromosome,
  plot_lines_distance = 0.03,
  vp = viewport(x = 0, y = 0.95, just = c("left", "top")),
  splice_variants = TRUE,
  non_coding = TRUE
)

Arguments

`ensdb`	ENSEMBL database object like EnsDb.Hsapiens.v86
`minRange`	start genome coordinate
`maxRange`	end genome coordinate
`chromosome`	chrom
`plot_lines_distance`	veritcal distance between genes
`vp`	viewport
`splice_variants`	if TRUE, show multiple transcripts from the same gene
`non_coding`	if TRUE, also show non-coding genes

Value

GRanges object of exon locations

Examples

library(EnsDb.Hsapiens.v86)
library(GenomicRanges) 
library(grid) 

# gene database
ensdb = EnsDb.Hsapiens.v86

# interval
query = GRanges("20", IRanges(62045027,62164563))

# plot genes
fig = plotEnsGenes( ensdb, start(query), end(query), seqnames(query))
grid.draw( fig )

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.