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fwhelan / coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.
GNU General Public License v3.0
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Feature request: Heatmap output as gridded data (csv/tsv) #56

Closed amymariecampbell closed 1 year ago

amymariecampbell commented 2 years ago

It would be really helpful if, as well as the great visual output of the heatmap, this information could be provided in some kind of gridded data format- with rows representing samples and the columns representing the gene groups. The different clusters would perhaps need to be assigned numbers rather than colours which would be inputted into the cells where the colour blocks are in the tree. This would be really great for downstream analysis, particularly as I'm trying to work out any spatiotemporal links between the coincident genes. Hope that makes sense!

fwhelan commented 1 year ago

That makes complete sense and is a really great idea! This is already coded in the R code that generates the heatmap, so it was a pretty easy addition. I've just pushed it now and will make a new version of coinfinder now which will push to conda automatically.

Let me know if you run into any issues with it! And thank you for your patience.

amymariecampbell commented 1 year ago

Great thanks Fiona! Do we need to specify as an option or is it an automatic output?

fwhelan commented 1 year ago

Hi amymariecampbell. It's automatic, but note that you'll need the most recent version v1.2.1.

amymariecampbell commented 1 year ago

Is Version 1.2.1 available on Conda? I just tried to update but my version is still 1.1 Thanks again!

From: Fiona J Whelan @.> Sent: Friday, January 6, 2023 4:37 PM To: fwhelan/coinfinder @.> Cc: Amy Campbell (Cefas) @.>; Author @.> Subject: Re: [fwhelan/coinfinder] Feature request: Heatmap output as gridded data (csv/tsv) (Issue #56)

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Hi amymariecampbell. It's automatic, but note that you'll need the most recent version v1.2.1https://github.com/fwhelan/coinfinder/releases/tag/1.2.1.

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fwhelan commented 1 year ago

Hi amymariecampbell. Conda should at least be giving you 1.2.0 which was merged into bioconda in May 2022?

As for 1.2.1, I had labelled it as a pre-release so I don't think was automatically picked up by bioconda's bot to automerge it into bioconda. I've changed this now, so it should be updated in bioconda within 48hours; please let me know if it's not, though, and I'll follow up and merge it manually :).

Thanks!

fwhelan commented 1 year ago

Hi amymariecampbell. Sorry it took so long; bioconda's version of coinfinder should now be v1.2.1. Let me know if you still have any issues accessing it!

Thanks for your patience!