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PitchInteractiveInc / Phinch

Phinch is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project represents an interdisciplinary collaboration between Pitch Interactive, a data visualization studio in Oakland, CA, and biological researchers at UC Riverside.
http://phinch.org/
BSD 2-Clause "Simplified" License
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OTU Bubble Chart #66

Open iimog opened 7 years ago

iimog commented 7 years ago

In an earlier version of Phinch there has been a "Bubble Chart By OTU" still visible in the README at https://github.com/PitchInteractiveInc/Phinch. From what I get this chart contained one bubble per OTU (combined at a given taxonomic level) with internal bubbles representing the samples that contribute to this OTU. Has this chart been dropped from Phinch because it was found not to be useful or what else was the reason? I'm currently spending some time with the Phinch code and I was wondering if it is worth trying to resurrect this feature.

hollybik commented 7 years ago

We suspended work on the "bubble chart by OTU" visualization because of time constraints when we were building the prototype (it was going to require too much developer time to debug the code and get all the features properly implemented, and we had to shift our effort to more pressing features in the other 5 visualizations) - it is still an interesting features that I would like to resurrect in the future, so feel free to play around with it further. The original idea was to have an extremely fine-scale visualization that helped to look at occurrence patterns for individual OTUs (e.g. those OTUs which had the exact same presence/absence across samples or sites). This is just one example use case, but the rationale was to have a visualization that allowed you to look at "raw" data without summarizing by taxonomic level or lumping by metadata category.

iimog commented 7 years ago

Thanks for the clarification. I agree, that this kind of visualization can be very useful. If I find time I will try to implement it. I will let you know when I get started.

judithguitart commented 1 year ago

Hey there! I am using for the first time Phinch, and I think it is a great visualization tool for my metagenomic data! After the troubleshooting of generating a biom file with the metadata, I have been able to generate the bargraphs. However, I was wondering if the bubble charts or other graphs are activated, or how can I change my graph's type. Thank you very much in advance.