I’ve been struggling with the network analysis for a while even though it doesn’t seem complicated.
Regarding the data, I have an output from qiime2 - otu table converted from the biom file + relative abundance of resistance genes obtained with real-time PCR analysis.
What I actually want to do is to make a correlation between microbial communities and antibiotic resistance genes in order to assume potential hosts of resistance genes.
I found in papers that people first calculate Spearman’s rank correlation between ARG subtypes and microbial taxa. After that, they use significantly robust correlations to form the co-occurrence network with R packages vegan, igraph and Hmisc.
So, this doesn’t look very complicated, but my knowledge in R is pretty basic and I got stuck.
Thus, I would really like to ask for your help and R codes if anyone did that already.
Many thanks in advance.