genePlot {casper} | R Documentation

## 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

`generanges` | Object containing the ranges with start/end of each exon.
`islandid` | If `generanges` is not specified, transcripts are obtained from island `islandid` from the annotated genome `genomeDB`.
`genomeDB` | Annotated genome produced with the "procGenome" function
`reads` | `pbam` object with aligned reads. This is an optional argument.
`exp` | `ExpressionSet` object with expression values, as returned by `calcExp`. This is an optional argument.
`names.arg` | Optionally, indicate the names of each transcript.
`xlab` | x-axis label
`ylab` | y-axis label
`xlim` | x-axis limits, defaults to start of 1st exon and end of last exon
`cex` | Character expansion
`yaxt` | The y-axis in the plot has no interpretation, hence by default it is not displayed.
`col` | Either single color or vector of colors to be used to draw each transcript. Defaults to rainbow colors.
`...` | Other arguments to be passed on to `plot`.

### 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)

[Package casper version 2.20.0 Index]