checkAssembledTx {ballgown} | R Documentation

## 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).

### 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)

[Package ballgown version 2.14.1 Index]