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

In vjcitn/TxRegInfra2: Metadata management for multiomic specification of transcriptional regulatory networks, version 2

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/TxRegInfra2 documentation built on Jan. 1, 2021, 12:41 p.m.