Help to interpret plot_network output
0
1
Entering edit mode
6.2 years ago
DVR ▴ 30

Hello BioStars community,

I am working with my 16S data and I am having difficulties interpreting the result of make_network and plot_network with default options.

# source('http://bioconductor.org/biocLite.R')
# biocLite('phyloseq')

library('phyloseq')

b <- make_network(a, type="taxa",max.dis=0.5)
plot_network(b,a, type="taxa", label="Genus", color="Phylum")

I see that the default option uses distance="jaccard" and according to vegdist {vegan}, Jaccard index is computed as 2B/(1+B), where B is Bray–Curtis dissimilarity.

Can anyone help me to understand what taxa connection can be interpret?

Thanks

R bioconductor • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 1917 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6