R: Plot Splice Summary from RNA-seq data

plotSpliceSum {ggbio}

R Documentation

Plot Splice Summary from RNA-seq data

Description

Plot splice summary by simply counting overlaped junction read in weighted way or not.

Usage

## For character,GRangesList
## S4 method for signature 'character,GRangesList'
plotSpliceSum(data, model, ..., weighted = TRUE)
## For character,TranscriptDb
## S4 method for signature 'character,TranscriptDb'
plotSpliceSum(data, model, which,
      ..., weighted = TRUE)

Arguments

`data`	A character specifying the bam file path of RNA-seq data.
`model`	A GRangesList which represting different isoforms, or a TranscriptDb object. In the second case, users need to pass "which" argument which is a GRanges object to specify the region. And we get connonical model internally.
`which`	A GRanges object specifying the region you want to get model from the TranscriptDb object.
`weighted`	If `TRUE`, weighted by simply add 1/cases matched to each model and if `FALSE`, simply add 1 to every case.
`...`	Extra arugments passed to `qplot` function. such as, `offset` which control the height of chevron.

Details

Internally we use biovizBase:::spliceSummary for simple counting, but we encourage users to use their own robust way to make slicing summary and store it as GRangesList, then plot the summary by qplot function.

Value

A ggplot object.

Author(s)

Tengfei Yin

Examples

## Not run: 
##D bamfile <- system.file("extdata", "SRR027894subRBM17.bam", package="biovizBase")
##D library(TxDb.Hsapiens.UCSC.hg19.knownGene)
##D txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
##D data(genesymbol)
##D exons <- exonsBy(txdb, by = "tx")
##D exons.rbm17 <- subsetByOverlaps(exons, genesymbol["RBM17"])
##D plotSpliceSum(bamfile, exons.rbm17)
##D plotSpliceSum(bamfile, exons.rbm17, weighted = FALSE, offset = 0.01)
##D plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"])
##D plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"], offset = 0.01)
##D plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"],
##D               show.label = TRUE,
##D               label.type = "count")
## End(Not run)

[Package ggbio version 1.5.20 ]