R: plot annotated and assembled transcripts together
checkAssembledTx
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).
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(ballgown)
Attaching package: 'ballgown'
The following object is masked from 'package:base':
structure
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ballgown/checkAssembledTx.Rd_%03d_medium.png", width=480, height=480)
> ### Name: checkAssembledTx
> ### Title: plot annotated and assembled transcripts together
> ### Aliases: checkAssembledTx
>
> ### ** Examples
>
> ## No test:
> gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
> annot = gffReadGR(gtfPath, splitByTranscript=TRUE)
Warning in readGFF(filepath, version = version, filter = filter) :
connection is not positioned at the start of the file, rewinding it
> data(bg)
> checkAssembledTx(annotated=annot, assembled=structure(bg)$trans, ind=4)
> ## End(No test)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.