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

Description Usage Arguments Value Examples

View source: R/txmodels.R

Description

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

Usage

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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

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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.