Color alternative transcripts according to transcript type (retained intron, processed transcript, etc)

[luxeredias]

New feature

Most protein coding genes have several alternative splicing mRNA isoforms, many of which are not protein coding themselves (due to lack of ORF, premature stop codon, retained intro, etc). It would be interesting to be able to visualize which transcripts of a gene are of each "transcript type" (according to the Gencode annotation, for instance).

Usage scenario

Can be used when one wants to visually confirm which kind of transcripts of a gene are being more thouroghly expressed between conditions.

Suggest implementation

Include an argument in the main function so the user can choose whether to use it or not.
Functions that ought to be altered to receive this implementation are probably:
read_gtf(): return information on the transcript type of each transcript (lines 276-305)
gtf_for_plot(): include another column in the dataframe that will be used by ggplot2 to plot the GTF plot bellow tha main sashimi plot (lines 348-436)