geneViz: Construct a gene-features plot

Description

Given a GRanges object specifying a region of interest, plot genomic features within that region.

Usage

geneViz(txdb, gr, genome, reduce = FALSE, gene_colour = NULL, base = c(10, 2, 2), transform = c("Intron", "CDS", "UTR"), isoformSel = NULL, labelTranscript = TRUE, labelTranscriptSize = 4, plotLayer = NULL)

Arguments

txdb

Object of class TxDb giving transcription meta data for a genome assembly. See Bioconductor annotation packages.

Object of class GRanges specifying the region of interest and corresponding to a single gene. See Bioconductor package GRanges.

genome

Object of class BSgenome specifying the genome sequence of interest. See Bioconductor annotation packages.

reduce

Boolean specifying whether to collapse gene isoforms within the region of interest into one representative transcript. Experimental use with caution!

gene_colour

Character string specifying the colour of the gene to be plotted.

base

Numeric vector of log bases to transform the data corresponding to the elements supplied to the variable transform See details.

transform

Character vector specifying what objects to log transform, accepts "Intron", "CDS", and "UTR" See details.

isoformSel

Character vector specifying the names (from the txdb object) of isoforms within the region of interest to display.

labelTranscript

Boolean specifying whether to plot the transcript names in the gene plot.

labelTranscriptSize

Integer specifying the size of the transcript name text in the gene plot.

plotLayer

Valid ggplot2 layer to be added to the gene plot.

Value

object of class list with list elements containing a ggplot object, the gene features within the plot as a data frame, and mapping information of the gene features within the ggplot object.

Details

geneViz is an internal function which will output a list of three elements. As a convenience the function is exported however to obtain the plot from geneViz the user must call the first element of the list. geneViz is intended to plot gene features within a single gene with boundaries specified by the GRanges object, plotting more that one gene is advised against.

Typically, introns of a transcript are much larger than exons, while exons are sometimes of greater interest. To address this, genCov will by default scale the x-axis to expand track information according to region type: coding sequence (CDS), untranslated region (UTR), or intron / intergenic (Intron). The amount by which each region is scaled is controlled by the `base` and `transform` arguments. `transform` specifies which regions to scale, and `base` corresponds to the log base transform to apply to those regions. To keep one or more region types from being scaled, omit the corresponding entries from the `base` and `transform` vectors.

Examples

Run this code

# need transcript data for reference
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

# need a biostrings object for reference
library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19

# need Granges object
gr <- GRanges(seqnames=c("chr10"),
ranges=IRanges(start=c(89622195), end=c(89729532)), strand=strand(c("+")))

# Plot the graphic
geneViz(txdb, gr, genome)

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