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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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Visualize observation metadata #61

Open iimog opened 8 years ago

iimog commented 8 years ago

The visualization of observation metadata seems to be limited to taxonomic information. The wiki (https://github.com/PitchInteractiveInc/Phinch/wiki/Visualization-Gallery#taxonomy-bar-chart) suggests that:

The Taxonomy Bar Chart can be used to display the community compositions (or gene ontologies, or other observation data) present across samples.

The same applies for the Bubble Chart. However both testing (with biom files that include observation metadata) and looking at the code indicate that Phinch can only handle taxonomy data. It worked to pass the metadata as fake taxonomy (the real taxonomy is lost in this case).

Is it possible to toggle between the type of metadata to use from the biom file?

hollybik commented 8 years ago

Currently any type of metadata attributed to each OTU would need to be imported as "fake taxonomy", as you indicate - other metadata at the sample level would be added at the end of the BIOM file and apply to ALL OTUs found within a samples.

Thanks for pointing this out - hopefully we can add support for toggling in between metadata/ontologies in future versions of Phinch. I'll leave this issue open for now.