phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
I suspect this question has a super simple solution, but I have had a hard time figuring out a good workflow. Thanks in advance, and apologies for the basic request.
I want to tabulate and visualize, by treatment, the most abundant taxa or ASVs - I say both here because many of the sequences in my dataset are uncultured/unclassified, so show up as distinct bands in abundance plots but have no distinguishing taxonomic designation.
My end goal is to create a table listing the top n taxa in each of two treatments ("impacted"/"unimpacted"), the relative abundance of each of those taxa in each treatment, and whether each taxa shows up in only one or in both treatments. The visualization is less important than the table - if folks have suggestions for displaying this information using e.g. a Venn diagram or something similar that would be helpful, but I can make do with the barplots I've been able to produce already.
Hi all,
I suspect this question has a super simple solution, but I have had a hard time figuring out a good workflow. Thanks in advance, and apologies for the basic request.
I want to tabulate and visualize, by treatment, the most abundant taxa or ASVs - I say both here because many of the sequences in my dataset are uncultured/unclassified, so show up as distinct bands in abundance plots but have no distinguishing taxonomic designation.
My end goal is to create a table listing the top n taxa in each of two treatments ("impacted"/"unimpacted"), the relative abundance of each of those taxa in each treatment, and whether each taxa shows up in only one or in both treatments. The visualization is less important than the table - if folks have suggestions for displaying this information using e.g. a Venn diagram or something similar that would be helpful, but I can make do with the barplots I've been able to produce already.
Any suggestions are greatly appreciated!