Plot exon structure for each transcript of a given gene.

Description

Plot exon structure for each transcript of a given gene. Optionally, aligned reads can be added to the plot.

Usage

genePlot(generanges, islandid, genomeDB, reads, exp, names.arg, xlab='',
ylab='', xlim, cex=1, yaxt='n', col, ...)

Arguments

Value

A plot is produced.

Methods

signature(generanges="CompressedIRangesList", islandid="ANY", genomeDB="ANY", reads="ANY", exp="ANY")

Plots a set of transcripts. Each element in the generanges corresponds to a transcript. Each transcript should contain exon start/end positions.

signature(generanges="IRanges", islandid="ANY", genomeDB="ANY", reads="ANY", exp="ANY")

Plots a single transcript. Each range indicates the start/end of a single exon.

signature(generanges="IRangesList", islandid="ANY", genomeDB="ANY", reads="ANY", exp="ANY")

Plots a set of transcripts. Each element in the generanges corresponds to a transcript. Each transcript should contain exon start/end positions.

signature(generanges="GRangesList", islandid="ANY", genomeDB="ANY", reads="ANY", exp="ANY")

Plots a set of transcripts. Each element in the generanges corresponds to a transcript. Each transcript should contain exon start/end positions.

signature(generanges="GRanges", islandid="ANY", genomeDB="ANY", reads="ANY", exp="ANY")

Plots a set of transcripts. Each space in generanges corresponds to a transcript. Each transcript should contain exon start/end positions.

signature(generanges="missing", islandid="character", genomeDB="annotatedGenome", reads="GRanges", exp="ExpressionSet")

Plots all transcripts stored in genomeDB for island with identifier islandid. Individual reads are added to the plot (reads contains start/end of individual read fragments).

signature(generanges="missing", islandid="character", genomeDB="annotatedGenome", reads="missing", exp="missing")

Plots all transcripts stored in genomeDB for island with identifier islandid.

signature(generanges="missing", islandid="character", genomeDB="annotatedGenome", reads="procBam", exp="missing")

Plots all transcripts stored in genomeDB for island with identifier islandid. Individual reads are added to the plot (reads contains start/end of individual read fragments).

signature(generanges="missing", islandid="character", genomeDB="annotatedGenome", reads="procBam", exp="ExpressionSet")

Plots all transcripts stored in genomeDB for island with identifier islandid. Individual reads and estimated expression are added to the plot (reads contains start/end of individual read fragments).

Author(s)

Camille Stephan-Otto Attolini, David Rossell

Examples

data(hg19DB)

#Plot an IRangesList
txs <- transcripts(txid="NM_005158",genomeDB=hg19DB)
genePlot(txs)

#Equivalently, indicate islandid
islandid <- getIsland(txid="NM_005158",genomeDB=hg19DB)
genePlot(islandid=islandid, genomeDB=hg19DB)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(casper)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/genePlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genePlot
> ### Title: Plot exon structure for each transcript of a given gene.
> ### Aliases: genePlot genePlot-methods
> ###   genePlot,CompressedIRangesList,ANY,ANY,ANY,ANY-method
> ###   genePlot,IRanges,ANY,ANY,ANY,ANY-method
> ###   genePlot,GRangesList,ANY,ANY,ANY,ANY-method
> ###   genePlot,IRangesList,ANY,ANY,ANY,ANY-method
> ###   genePlot,GRanges,ANY,ANY,ANY,ANY-method
> ###   genePlot,missing,character,annotatedGenome,GRanges,ExpressionSet-method
> ###   genePlot,missing,character,annotatedGenome,missing,missing-method
> ###   genePlot,missing,character,annotatedGenome,procBam,ExpressionSet-method
> ###   genePlot,missing,character,annotatedGenome,procBam,missing-method
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(hg19DB)
> 
> #Plot an IRangesList
> txs <- transcripts(txid="NM_005158",genomeDB=hg19DB)
> genePlot(txs)
> 
> #Equivalently, indicate islandid
> islandid <- getIsland(txid="NM_005158",genomeDB=hg19DB)
> genePlot(islandid=islandid, genomeDB=hg19DB)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>