Entering edit mode
3.7 years ago
mail2steff
▴
70
Dear All, I have OTU table obtained from qiime2 analysis and imported into phyloseq. I would like to get the unifrac distance between pair-wise species (not between the samples). in the output, I need distance matrix between the OTUs
OTU1 OTU2 OTU3 OTU4 OTU5
OTU1 1 0.023 0.045 0.12 0.034
OTU2 : : : : :
OTU3 : : : : :
OTU4 : : : : :
OTU5 : : : : :
So I tried as follows:
unifrac_distance<-distance(ps, method="unifrac", type = "taxa")
But still I am getting matrix between the samples. How do I achieve OTU-wise unifrac distance matrix?
I searched found this: UniFrac distance and DPCoA cannot be calculated for taxa-wise distances, because they use a taxa-wise tree as part of their calculation between samples, and there is no transpose-equivalent for this tree.