Any Package in R for Highliting Key Taxa in Family levels?

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1

Hi all,
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.
Many thanks
Qiimer

2

Hello again,

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:
https://joey711.github.io/phyloseq/preprocess.html

Colin

4

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?
Qiimer

5

Happy to help!

Phyloseq objects can contain metadata table, features table, taxonomy table, phylogenetic tree, and a feature's sequences.
https://joey711.github.io/phyloseq/import-data.html#phyloseq-ize_data_already_in_r

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.

Colin

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