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,TxDb
    ## S4 method for signature 'character,TxDb'
    plotSpliceSum(data, model, which,
          ..., weighted = TRUE)
    ## For character,EnsDb
    ## S4 method for signature 'character,EnsDb'
    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, a TxDb or an `EnsDb` object. For the latter cases, users need to pass "which" argument which, for TxDb, is a GRanges object to specify the region and for `EnsDb` can be a GRanges object, an object extending `AnnotationFilter`, an `AnnotationFilterList` combining such filter objects or a filter expression in form of a `formula`.
`which` | A GRanges object specifying the region you want to get model from the TxDb object. For `EnsDb`: can be a GRanges object, an object extending `AnnotationFilter`, an `AnnotationFilterList` combining such filter objects or a filter expression in form of a `formula`.
`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

### See Also

`qplot`

### Examples

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

    ## End(Not run)

[Package ggbio version 1.38.0 Index]