R/txmodels.R

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

#' use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation
#' @param sym a gene symbol to be looked up in biovizBase::genesymbol table
#' @param gr a GRanges instance, anticipated to be length 1
#' @param edb a character(1) name of an EnsDb annotation package
#' @param plot.it a logical(1) specifying whether Gviz::plotTracks should be run
#' @param radius a numeric(1) specifying number to add to IRanges instance used to subset gene models from ensembldb::exonsBy output
#' @return an instance of Gviz::GeneRegionTrack, invisibly returned
#' @param \dots passed to Gviz::GeneRegionTrack
#' @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)
#' @export
txmodels = function(sym, gr, edb = "EnsDb.Hsapiens.v75", plot.it = FALSE, radius = 0, 
    ...) {
    suggInst = function(pname) {
        if (!requireNamespace(pname)) 
            stop(sprintf("please install package %s to use txmodels.", pname))
    }
    suggInst("biovizBase")
    suggInst("ensembldb")
    suggInst("GenomeInfoDb")
    suggInst("Gviz")
    suggInst("AnnotationFilter")
    if (sum(c(missing(sym), missing(gr))) != 1) 
        stop("exactly one of sym, gr must be nonmissing")
    require(edb, character.only = TRUE)  # FIXME
    if (!missing(sym)) {
        gr = biovizBase::genesymbol[sym]
    }
    GenomeInfoDb::seqlevelsStyle(gr) = "Ensembl"
    seq = as.character(GenomeInfoDb::seqnames(gr))[1]
    eg <- ensembldb::exonsBy(get(edb), by = "tx", filter = AnnotationFilter::AnnotationFilterList(AnnotationFilter::SeqNameFilter(c(seq)), 
        AnnotationFilter::GeneIdFilter("ENS", "startsWith")), columns = c("gene_biotype", 
        "gene_name", "tx_id"))
    eg2 = as.data.frame(IRanges::subsetByOverlaps(eg, gr + radius))
    eg2$chromosome = eg2$seqnames
    eg2$symbol = eg2$gene_name
    eg2$exon = eg2$exon_id
    eg2$transcript = eg2$transcript_id
    eg2$feature = eg2$gene_biotype
    eg2$gene = eg2$gene_name
    eg2$transcript = eg2$tx_id
    grt = Gviz::GeneRegionTrack(eg2, ...)
    if (plot.it) 
        Gviz::plotTracks(list(Gviz::GenomeAxisTrack(), grt), showId = TRUE)
    invisible(grt)
}