search

Oshlack / Clinker

Gene Fusion Visualiser
MIT License
51 stars 12 forks source link

Plot with multi-samples #14

Open maximillo opened 5 years ago

maximillo commented 5 years ago

Dear Breon,

Thanks for developing this brilliant package for the community! I really like the final layout of the plot and would like to adapt it to my own project to look at the TMPRSS2-ERG fusions in prostate cancer patients. I've managed to get the pipeline to run on a one-by-one basis but have not figured out how you pulled off the multi-sample plots for P2RY8-CRLF2 as you shown in your paper. Not sure if I missed it in this repository. If you did it with an independent script, any chance you can share? Thanks a lot!

Regards, Max

breons commented 5 years ago

Hi Max,

Thank you for your kind words, I'm really happy that people are getting some use out of it!

That final layout was a bit manual for that specific case, basically I played around with the fst_plot.r file to stack all of the necessary components together, then used photo-editing software to highlight the junctions found across the fusion pairs in each of the six samples.

However, I've always thought I could just add this as a parameter, a multi-clinker option! I might have to think of a more clever way to put in the sashimi lines, given they're not natively oriented this way, but there will be a way I'm sure.

If you're really keen to have this, leave it with me and I will add it to clinker 1.4.

Cheers, Breon.

maximillo commented 5 years ago

Hi Breon,

This sounds awesome! I'd love to have that option in your upcoming release. This would enable us to have a much more effective visual inspection on the different fusions from different patients. I very much look forward to getting my hands on it!

Thanks again & Happy coding :)

Max

breons commented 5 years ago

My pleasure!

Once I finish this feature I will make sure it's available on the development branch, so you can trial it before the next release anyway. Hopefully you will have something next month.

Happy coding :)

Always!

breons commented 5 years ago

Hi Max,

Just letting you know I haven't forgotten about you. Busy month. Apologies for the delay!

Breon.

maximillo commented 5 years ago

No worries, Breon. Please take care of your priorities first and keep me posted if anything. Thanks a lot!

Max