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