txmodels: use Gviz to render transcript models via GeneRegionTrack, but...

In vjcitn/TxRegInfra: Metadata management for multiomic specification of transcriptional regulatory networks

Description

use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation

Usage

txmodels(sym, gr, edb = "EnsDb.Hsapiens.v75", plot.it = FALSE,
  radius = 0, ...)

Arguments

sym	a gene symbol to be looked up in biovizBase::genesymbol table
gr	a GRanges instance, anticipated to be length 1
edb	a character(1) name of an EnsDb annotation package
plot.it	a logical(1) specifying whether Gviz::plotTracks should be run
radius	a numeric(1) specifying number to add to IRanges instance used to subset gene models from ensembldb::exonsBy output
...	passed to Gviz::GeneRegionTrack

Value

an instance of Gviz::GeneRegionTrack, invisibly returned

Examples

t0 = txmodels('ORMDL3', plot.it=TRUE, name='ORMDL3')
t1 = txmodels('ORMDL3', plot.it=FALSE, name='meta', collapseTranscripts='meta')
requireNamespace('Gviz')
Gviz::plotTracks(list(Gviz::GenomeAxisTrack(), t0, t1), showId=TRUE)

vjcitn/TxRegInfra documentation built on July 6, 2019, 10:47 p.m.