Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Visualize observation metadata #61

Open
iimog opened this issue Jun 13, 2016 · 1 comment
Open

Visualize observation metadata #61

iimog opened this issue Jun 13, 2016 · 1 comment

Comments

@iimog
Copy link
Contributor

iimog commented Jun 13, 2016

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
Copy link
Collaborator

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants