high-level workflow example

[gpertea]

Thank you for this excellent work - I have been looking for something like this for a while as I often needed to explore transcript assemblies within a gene or genomic region while comparing them with reference annotation etc.

I think it would be really useful for the community (and increase the popularity/adoption of the package) to provide a step-by-step workflow example (perhaps adding a few high-level convenience functions) for a use case like this:

• loading a user provided GTF/GFF or BED file (e.g. with novel transcripts). As far as I know this can be done starting with something like as.data.frame(rtracklayer::import("user.gtf"))
• loading reference annotation transcripts for the specified region of interest (or a gene?), from the available AnnotationDbi (orgdb) and txdb packages out there, or pulling such annotation directly from an online resource (biomaRt); in general
• display the above with ggtranscript in a visually distinct manner (the reference transcripts using a different color from the user loaded transcripts, or otherwise suggesting/delimiting the two separate "tracks")

A genomic range would of course be required from the start (could be also used to subset the transcripts from the user provided file), with some common-sense checks (if not already implemented) to limit the genomic region width, the maximum number of transcripts etc.

[dzhang32]

I'm super glad you find ggtranscript useful :)

Thanks for the detailed description - I completely agree, this workflow would be very helpful for users, will work on adding.