Filtering gneiss balances shown on heatmap


(Jennifer Jankowiak) #1

HI,

Is there a way to filter which balances are shown on the Gneiss dedrogram_heatmap visualizations so you can choose to display balances of interest (i.e. significant balances) instead of the default by numeric order? If not is there a way to export the balances to replicate a similar plot in another program such as R?

Thanks in advance for any help


(Nicholas Bokulich) assigned mortonjt #2

(Jamie Morton) #3

The Gneiss dendrograms are not very flexible, so it is currently not possible to specify other balances of interest.

That being said, you can totally import the balances to another program - just unpack the tree and the balances artifacts and load into your own custom script. Calour should have more customizable tree visualization capabilities.

But if you figure out a way to feed the exported data into anvio, that would be truly amazing

See the exporting data tutorial on more information on extract data from artifacts.


(Nicholas Bokulich) unassigned mortonjt #4

(Jennifer Jankowiak) #5

Thanks Jamie for introducing me to these new tools they look very useful and I can’t wait to try them. I did some paying around with the Artifact API and was able to make the same figure as the gneiss-dendrogram plugin but indexing the balances i was interested in following this tutorial: https://biocore.github.io/gneiss/docs/v0.4.0/tutorials/python/cfs-python-tutorial.html
As someone who had never used the python or the API before it took a while to actually figure out how to access it from a virtual machine ( I did not realize it was as simple as running Jupyter-notebook in the terminal command line) but after that the qiime API tutorials were very helpful.

I would still like to figure out how to order my samples and these new tools look like they will be helpful for that.

I appreciate the help!