Generate a heatmap using unweighted unifrac distance matrix

heatmap

#1

Hello!

I am relatively new to using QIIME 2. I currently use the the 2018.4 version. I recently used the beta rarefaction analysis to produce the jackknifed emperor plot, heatmap, and clustered phylogenetic tree using the unweighted unifrac distance matrix. I am wondering if there is a way that I could produce a different heatmap that also uses the unweighted unifrac distance matrix so that I may use it alongside my analysis of the clustered phylogenetic tree.


(Nicholas Bokulich) #2

Hi @Bookworm1225! I am not sure I 100% understand what you are trying to accomplish, but here goes. Sounds like you want to generate a heatmap showing the pairwise distances between each sample. QIIME 2 has no such stand-alone visualization… but if you know a bit of python this heatmap would be very easy to generate using scikit-bio. Just do something like the following (e.g., in an iPython notebook; note I am not testing this, just writing from memory, and you should see the scikit-bio documentation if you run into trouble):

import qiime2
import skbio

dm = qiime2.Artifact.load('unweighted_unifrac_distance_matrix.qza')
dm.view(skbio.DistanceMatrix)

#3

Hello!

I am not familiar with using Python in this way, but I will definitely give it a try! Thank you for the help!


(system) closed #4

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