Heatmapping Beta diversity

General Discussion
1

Hi all, newcomer to both qiime2 and microbial science here.

I'm wondering (and not finding an answer in either qiime2 docs or the forum) whether it's possible in qiime2 to produce a heatmap where both x and y axes represent samples (designated 1 to 20, let's say) and colour shades at the crossing represent the value of selected Beta-diversity metric.

I have the core Beta diversity metrics computed in qiime2 for my samples so I have everything needed as input, I believe. This should be a simple feat to achieve, the question is through which plugin?

Thanks in advance for any ideas!

Cheers

Jan

2

Hi @Jan_Kollar ,

QIIME 2 does not have such a function itself, but it is easy to make one by passing a QIIME 2 distance matrix to the python package scikit-bio.

Give the following a try (working example from a Jupyter Notebook, will need some tweaks to run outside of a notebook):

import qiime2 as q2
import skbio
%matplotlib inline

dm = q2.Artifact.load('weighted_unifrac_distance_matrix.qza')
dm = dm.view(skbio.DistanceMatrix)
dm.plot()
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3

Thanks for your attention! I've already resolved the issue by simply exporting the distance matrices from the respective QIIME2 artefacts, feeding them to R and building the heatmaps there. Nevertheless, the suggested python-based solution is certainly more elegant and gives the same result, of course. Thanks a lot!

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