Some questions for Qiime2/R after "moving picture"

[jungsoo_Park]

Hi, I am a beginner of Qiime2 and recently started intensely learning microbial analysis by using both Qiime2 and Rstudio. I feel that Qiime2 is more straightforward and comfortable to me so far. But, sadly, it seems like that using R is still necessary for more options and controlling my results in a sophisticated manner…

1. I need Deseq2 and NMDS analysis that doesn’t seem to be available in Qiime2. Then, what’s the most convenient way to export post-DADA2 data and import in R? Does this way still benefit users instead of processing even dada2 in R environment?

2. I’ve made a taxonomy bar plot; I want to see only top 20 taxa and others (rest of the taxa). When I searched, it looks possible in a way of filtering out all taxa except for the top 20… but can’t find how to make a bar indicating “others”. Also, I like to see only rank5 taxa name, for example, I now see "k_bacteria__proteobacteria__ ~~, instead, I want something like “flavobacteriaceae” in a short version. Or, do users also usually do this job in R?

I appreciate having any feedback. As a newbie in this field, there is so much information and this makes me more confused about what methods and data analysis process I choose.

[colinbrislawn (Colin J Brislawn)]

Hello @jungsoo_Park,

Welcome to the Qiime 2 forums. Are are asking very good questions.

@jungsoo_Park

But, sadly, it seems like that using R is still necessary for more options and controlling my results in a sophisticated manner…

This is correct. Qiime 2 is a good place to start, but you need a fully featured programing language like R + Phyloseq or Python + Qiime2 API to get full control of your stats and graphs.

@jungsoo_Park

most convenient way to export post-DADA2 data and import in R?

Try qiime2R! -> R

@jungsoo_Park

I’ve made a taxonomy bar plot; I want to see only top 20 taxa and others (rest of the taxa). When I searched, it looks possible in a way of filtering out all taxa except for the top 20… but can’t find how to make a bar indicating “others”. Also, I like to see only rank5 taxa name, for example, I now see "k_bacteria__proteobacteria__ ~~, instead, I want something like “flavobacteriaceae” in a short version. Or, do users also usually do this job in R?

I would make this graph using R or Python.

Let us know if you have any questions.

Colin