Rarefaction curve plots with genes and transcript categories

[JBerthelier]

Dear isotools authors,

I am wondering if it is possible to display gene and transcripts for the rarefaction curve on the same graph. An example of figure : https://github.com/Magdoll/cDNA_Cupcake/blob/master/annotation/test_data/Rplot_test.all.gene_vs_isoform.min_fl_2.png

Also if it is possible to display the different category of transcripts similar to what is done from the SQANTI categories. An example of figure : https://github.com/Magdoll/cDNA_Cupcake/blob/master/annotation/test_data/Rplot_test.by_cat.isoforms.min_fl_2.png

I tried to produce such plots with isotools by modifiying the option of isotools but failed. It would so much quick to produce these graph with your tool.

Thank you

[MatthiasLienhard]

Dear Jérémy,

thanks for reaching out. While such functionality is not directly implemented, at least the second point would be quite straight forward to achieve with isotools. The Transcriptome.rarefaction function accepts filter terms to specify the categories, and returns a dataframe. These can be then used to plot the curves. Gene level rarefaction is currently not implemented, but would be not difficult either, following the code for transcripts. (_transcriptome_stats.py line 715 (rarefaction))

We are currently transferring the repository to https://github.com/HerwigLab/IsoTools2, so if you need additional support, please open another issue there.