plotGvizTracks: Plot coverage and gene model tracks

In csoneson/iResViewer: Interactive visualization of differential expression results

Description

Plot coverage and gene model tracks

Usage

plotGvizTracks(showGene = NULL, geneModels = NULL, geneModels2 = NULL,
  gtfFile = NULL, bwFiles = NULL, bwCond = NULL, showChr = NULL,
  minCoord = NULL, maxCoord = NULL, pdfFilename = NULL, pdfWidth = 7,
  pdfHeight = 7, ...)

Arguments

showGene	Gene name or symbol for the gene to show in the plot.
geneModels	GRanges object with gene models, typically generated from a gtf file (e.g. with the createGenemodels function).
geneModels2	Second GRanges object with gene models, e.g. those that were excluded from geneModels.
gtfFile	GTF file from which geneModels can be generated if it is not explicitly provided.
bwFiles	Named vector with paths to bigWig files. These will be used to generate coverage plots.
bwCond	Named vector corresponding to bwFiles, giving the group label for each bigWig file. These will be used to color the coverage plots by group.
showChr	Name of the chromosome to show in the plot, if showGene is not specified.
minCoord, maxCoord	Minimum and maximum genomic coordinate to show, if showGene is not specified.
pdfFilename	File name of pdf file to which the plot should be saved. If set to NULL, the plot is written to the current graphics device.
pdfWidth, pdfHeight	Width and height of the pdf file to which the plot should be saved.
...	Additional arguments (not currently used)

Author(s)

Charlotte Soneson

csoneson/iResViewer documentation built on May 28, 2019, 7:49 p.m.