I need a R package to extract key taxa in family level. HeatMap of family level in Feature Table is too long and not informative, so it is required to use a R package so that I get effective taxa in a table or plot and so on.
I use phyloseq for lots of my downstream visualizations. It includes functions like
subset_taxa(phyloseq.object, Phylum=="Chlamydiae") to filter out specific taxonomic levels.
There’s lots of good examples on this website:
Thanks a lot @colinbrislawn
You always helps us!
One question for you. I am not sure about the following questions.
Does Phyloseq package only need metadata and feature table? Does it need more files for example the rep-seq and taxonomy file? Should I use feature table with .qza file extension? Or I have to extract it?
Happy to help!
Phyloseq objects can contain metadata table, features table, taxonomy table, phylogenetic tree, and a feature’s sequences.
One good way to get data from Qiime2 into Phyloseq is to use the qiime2R package.
So the goal would be to import your Qiime2 artefacts as a Phyloseq object, then use the examples shown in the Phyloseq tutorials to subset down to your taxa of interest, and even maybe build a heatmap.