How to represent relative frequency of phyla in graph

User Support
1

Hi,

I do have relative frequency in the form of biom format from qiime2 by using the below command, I have multiple samples which belong to three groups: soil , root and shoot.

  1. How should I filter top10 variable phyla across these three groups in all samples and which tool should I use to make graph

qiime taxa collapse
--i-table feature-table.qza
--i-taxonomy taxonomy.qza
--p-level 2
--o-collapsed-table phyla-table.qza

Where feature-table.qza is from output of dada2/deblur and the taxonomy.qza file comes from the classifier I’ve linked above.

Now we will convert this new frequency table to relative-frequency:

qiime feature-table relative-frequency
--i-table phyla-table.qza
--o-realtive-frequency-table rel-phyla-table.qza

This new artifact now has the relative-abundances we want. To get this into a text file we first export the data which is in biom format:

qiime tools export rel-phyla-table.qza
--output-dir rel-table

Kind Regards

2

What kind of graph are you trying to make? I'm sorry, I wasn't quite able to follow the question here. Thanks!

3

Hi @thermokarst,

I want to represent relative frequency in the graph, instead of taking all phyla I just want to take 10 most abundant phyla.

and could you please suggest me what kind of other analysis I can do by using the relative frequency table.

Kind Regards

4

Good afternoon,

First, use qiime taxa collapse to get counts at the phyla level, then use qiime feature-table filter-features to get the top ten.

Let me know if this works for you!

Colin

P.S. Have you tried this plugin? It's really easy. barplot: Visualize taxonomy with an interactive bar plot — QIIME 2 2019.1.0 documentation

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5

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