genePlot: Plot exon structure for each transcript of a given gene.
In casper: Characterization of Alternative Splicing based on Paired-End Reads

Description Usage Arguments Value Methods Author(s) Examples

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

1 2	genePlot(generanges, islandid, genomeDB, reads, exp, names.arg, xlab='', ylab='', xlim, cex=1, yaxt='n', col, ...)

`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`.

A plot is produced.

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).

Camille Stephan-Otto Attolini, David Rossell

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)