plotGvizTracks: Plot coverage and gene model tracks

Description Usage Arguments Author(s)

Description

Plot coverage and gene model tracks

Usage

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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.