Hello!
I’m running a mantel test to determine if there are differences in the microbiomes of paired samples prepared using two different protocols: tissue homogenization vs wash only. I used this response to a forum post to set up my analysis and now I have a few questions about the interpretation of the mantel test.
The weighted unifrac and bray curtis distance matrixes were statistically significant with meaningful rho values (unweighted and jaccard were not statistically significant and had poor rho values).
Weighted:
Bray:
My two questions:
- What does the difference in data point color mean? All the points in the weighted graph (and unweighted and jaccard graphs not shown) are black, but most of them are blue in the bray graph. Is there a meaning behind the blue/black data points?
-
I checked the help documentation and checked the scikit-bio docs referenced in the help documentation, but neither had reference to colors/plotting.
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If it’s helpful, here’s the code I used to run the weighted test:
qiime diversity mantel --i-dm1 core-metrics-results_Tissue_grpd/weighted_unifrac_distance_matrix.qza --i-dm2 core-metrics-results_
Wash_grpd/weighted_unifrac_distance_matrix.qza --p-method 'spearman' --p-permutations 999 --p-label1 'Tissue' --p-label2
'Wash' --o-visualization out_mantel/vis_weighted_Tissue-Wash.qzv
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- Am I correct in interpreting these results as such: since both weighted unifrac and bray have significant and strong correlations that the tissue and wash protocol types produce similar compositions of microbes that is driven by similarities in microbial abundances? Is that over-interpreting?
Thank you!
~Samantha
P.S. The link provided in the mantel help documentation for the scikit-bio doc gives a HTTP 404 error. I think this is the updated link. Or at least it’s the one I used/found lol 