Top ten genus barplot

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1

Hi,

I need to create barplot with top ten genus.
The current barplot created with QIIME allows us to check with different taxa level but is there any way to only get top 10 or 20 of a genus or any taxa level?

I saw someone recommend to filter-features but that will only limit the number of samples included in the barplot but not the genus, correct?

Any help is really appreciated! Thank you.

2

You can try these things, but this is an independent solution that I would try. Maybe there is a way with qiime that I don't know of.

  1. You get a collapsed table at genus level with qiime taxa collapse, and then export it to get the biom file.

  2. biom convert -i feature-table.biom -o table.tsv --to-tsv

This would get you a tsv file including taxa at genus level which you can operate on and generate plots.

  1. I like plotly, since you can use it with R, python or Javascript. Create your own script to manipulate the data and to get any plot you would like.

Again, this might be overdoing things but I like to find my own way.

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filter-features will filter out features, not samples, from your table. So this would be an appropriate method to use:

  1. use qiime taxa collapse to collapse at genus level
  2. use qiime feature-table summarize to view a summary of the feature table and see the top 10 genera
  3. use qiime feature-table filter-features to filter based on sequence depth, selecting a cutoff that will exclude the less abundant taxa.

note that this will adjust the relative frequencies though... so making a customized plot outside of QIIME 2 as @the_dummy recommends is probably the better way to go for making a "top 10" plot that conserves the original relative frequencies.

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