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bartongroup / RATS

Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
MIT License
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Plot gene models #44

Closed fruce-ki closed 5 years ago

fruce-ki commented 6 years ago

Given a GTF/GFF or GRanges with full GTF metadata, show the exon structure of the isoforms. This would be a highly valuable complement to the current plot_genes(), as splicing patterns can add crucial information in interpreting shifts or variability in the abundances.

Being able to get this view easily, without requiring knowledge of Bioconductor structures and packages and writing several lines of code nor requiring an external genome browser would be very convenient, especially for RMarkdown reports and analyses.

fruce-ki commented 5 years ago

The GRanges derived from equivalent GTF and GFF3 appear to not be equivalent in the eyes of ggbio plotting functions. The GTF make passable transcript models, the GFF3 crashes with errors if I use the gene's GRangesList or produces ugly nearly nonsensical plots if I use a transcript's GRanges. Further investigation required.

fruce-ki commented 5 years ago

It is easier to convert a GFF to a GTF using existing well tested parsers than it is to make a specialized GFF parser. It is not worth the time and hassle required.