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Published 20 hours ago • verified publisher icon paul-shannon

Custom chromosome color for GWAS track

Open ladyson1806 opened this issue 1 year ago • 4 comments

Hi @paul-shannon!

Last year, I pointed you out an issue about a color bug for GWAS tracks in igvR (the whole story here). It is still there in igvShiny. As you mentioned in the post, the igv.js team updated their code to solve the issue, so it could be great to get an update of that part of the code to use it in igvShiny.

Nevertheless, I actually found your code implementation way simpler to use. It could be nice to add this feature to the GWASTrack function of the igvShiny package.

Again, thank you so much for your hard work on these packages, and for keeping them maintained. Have a nice day,

Best regards - Savvy

ladyson1806 avatar Jun 26 '23 17:06 ladyson1806

@ladyson1806, Hi Savvy. I regret to say that I will not have time to work on this any time soon. I have just retired from the Institute for Systems Biology. I have new (non-biology) projects keeping me very busy - too busy to work on this.

Maybe you could take it on, submit a PR?

paul-shannon avatar Jun 26 '23 18:06 paul-shannon

Thank you for your quick answer @paul-shannon. For sure, I will make a try!

ladyson1806 avatar Jun 26 '23 19:06 ladyson1806

Hi, @ladyson1806.

What's the status of this issue? Do you still consider this feature a high priority? If so, do you want to help me with it :)?

gladkia avatar Jan 13 '24 10:01 gladkia

Hi @gladkia,

Sorry for the delay of my answer! Short answer, I don't think this specific feature is a super high priority. But there will be similar requests as mine for sure.

Suggestions:

  • Having only two colors (black and grey) to just distinct with minimum color information where each chromosome starts and ends.
  • Custom color based on the number of the chromosomes, similarly as the original feature (just make sure that the proposed palettes are color-blinded friendly).

There is no rush on this issue, but if you manage to add those options, I will use them for sure! Thank you!

I'm citing the library in my paper (currently under reviewed) and we have deployed a web page relying on this package, so I'm happy to help you on igvShiny's improvement.

The, you can use our study as a user-case example of this app!

Have a nice day - Savvy

ladyson1806 avatar Jul 11 '24 14:07 ladyson1806