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PhinchApp / Phinch

Phinch is a data visualization framework aimed at promoting novel explorations of large biological datasets (microbiomes, metagenomes, etc.). Features include support for HDF5 and JSON BIOM files, retooled visualizations, improved image export and sharing, and the ability to work offline.
BSD 2-Clause "Simplified" License
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Giant brainstorm thread - your ideas for microbial ecology data visualizations! #5

Open hollybik opened 6 years ago

hollybik commented 6 years ago

What types of data visualizations would be useful for the analysis or interpretation of your microbial ecology or metabarcoding datasets? We want ideas for data visualizations that would be useful for researchers, educators, citizen scientists, and any other type of end users (e.g. technical to lay audiences).

Brainstorm your ideas below (and feel free to include example figures/images/etc. to help illustrate your point). Let us know what frustrates you with visualizations in existing tools (QIIME, phloseq, R packages, etc.) and tell us about data viz tools/ideas that don't currently exist.

manasvil commented 6 years ago

I was at a Data Vis meetup in NY and they were talking about unusual data visualizations in the lift sciences and here were some that were interesting:

Target Plot img_20180507_193119

Volcano plot img_20180507_193404

Ellipse Plot mvimg_20180507_193812

I am going to try and find some examples with explanations so they're more useful. But for now leaving this here.

manasvil commented 6 years ago

@hollybik I ended up writing a post about Target plots: https://medium.com/axis-group-visual-analytics-practice/that-which-we-call-a-target-plot-e295587009a9 in case you ever need more detail on what they are. Funny enough, I could not find much material on them during my search.

tomarashish commented 5 years ago

Hi @hollybik

I created a prototype web app for metagenomics data comparison using sunburst. The Web app shows the reference taxonomy as a tree view and multiple samples taxonomy hierarchy as sunburst. Following is a screenshot of the web app. Will like to know your view?

tree_view

tomarashish commented 5 years ago

Hi @hollybik Will like to hear from you about the visualization mentioned above.

hollybik commented 5 years ago

Hi @tomarashish, thanks for the examples - in the original Phinch framework we did have a tree view type visualization (called Sankey diagrams). The sunburst idea is also interesting. I'll pass on this idea to our developers to see if we might be able to incorporate something similar into the new Phinch desktop app.

geboro commented 5 years ago

The donut-partition visualization that was available in Phinch v1 was very clear for exploratory comparative analyses. Also, the bubble charts were very useful when talking to non-academic audiences.

hollybik commented 5 years ago

Thanks for the above feedback! We'll keep this in mind as we move forward with new visualization features for the Phinch desktop app.