How to perform and interpret PCA and NMDS analysis of soil fertility parameters with metagenome microbial community ? Please explain taking random datasets
Dear Laliteshwari Bhardwaj,
To do the PCA or NMDS analysis you can use the PAST software (https://www.nhm.uio.no/english/research/resources/past/)
To interpret the results you can consult the GUSTA ME (https://sites.google.com/site/mb3gustame/home?overridemobile=true)
I reckon you're trying to correlate environmental variables, sample_data of phyloseq, with the OTU table abundances (or ASVs whichever suits your data). If that is the case, using R, you can do it using the package microviz (https://david-barnett.github.io/microViz/).
Microviz has a shiny webapp which prompts a GUI that can be easily used, provided your phyloseq object is properly formatted.
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