plotSpliceSum: Plot Splice Summary from RNA-seq data

In tengfei/ggbio: Visualization tools for genomic data

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)

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.