ballgown (version 2.4.2)

checkAssembledTx: plot annotated and assembled transcripts together

Description

plot annotated and assembled transcripts together

Usage

checkAssembledTx(assembled, annotated, ind = 1, main = "Assembled and Annotated Transcripts", customCol = NULL)

Arguments

assembled

a GRangesList object where the GRanges objects in the list represent sets of exons comprising assembled transcripts

annotated

a GRangesList object where the GRanges objects in the list represent sets of exons comprising annotated transcripts

ind

integer; index of annotated specifying which annotated transcript to plot. All transcripts (assembled and annotated) overlapping annotated[[ind]] will be plotted. Default 1.

main

optional character string giving the title for the resulting plot. Default: "Assembled and Annotated Transcripts"

customCol

optional vector of custom colors for the annotated transcripts. If not the same length as the number of annotated transcripts in the plot, recycling or truncation might occur.

Value

Plots annotated transcripts on the bottom panel (shaded in gray) and assembled transcripts on the top panel (shaded with diagonal lines).

Examples

gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
annot = gffReadGR(gtfPath, splitByTranscript=TRUE)
data(bg)
checkAssembledTx(annotated=annot, assembled=structure(bg)$trans, ind=4)