checkAssembledTx: plot annotated and assembled transcripts together

In ballgown: Flexible, isoform-level differential expression analysis

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).

Author(s)

Alyssa Frazee

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)

ballgown documentation built on Nov. 8, 2020, 5:46 p.m.