q2-krona: Plugin for creating Krona plots

Hello everyone,

I've finally got time from work and finished the plugin. :tada:

Special thanks to @Nicholas_Bokulich for suggesting making my own plugin, and @thermokarst for revision.

The plugin is available at my github page (see: https://github.com/kaanb93/q2-krona).

Simply, Krona is a tool to create interactive multi-layered pie charts. Here is an example view of the chart below.

q2-krona is developed to make is easy to generate Krona plots, because the tool needs some rearrangement on FeatureTable[Frequency] to be able to work.

For now, the plugin consists of one visualizer and one pipeline. There might be some additions later on.

PLOT

This visualizer takes FeatureTable[Frequency] as input. But, I strongly suggest to use a collapsed table because this visualizer does NOT use reference taxonomy.

COLLAPSE AND PLOT

This pipeline uses taxa collapse method to use reference taxonomy with FeatureTable[Frequency] taken as input and krona plot visualizer to generate Krona plots. Collapse level and taxonomy delimiter are definable.

Here, I used feature table filtered to 2k minimum frequency and taxonomy from Parkinson's Mouse Tutorial to test the plugin.

Files:
https://docs.qiime2.org/2021.8/data/tutorials/pd-mice/table_2k.qza
https://docs.qiime2.org/2021.8/data/tutorials/pd-mice/taxonomy.qza

 qiime krona collapse-and-plot \
--i-table table_2k.qza \
--i-taxonomy taxonomy.qza \
--o-krona-plot krona.qzv

Output:
krona.qzv (401.0 KB)

The visualizer is viewable at QIIME 2 View.

Hope this plugin helps all QIIMErs. I can take suggestions/critiques on this forum or the github page.

Best wishes,

10 Likes

Hi @the_dummy,
Brilliant thanks so much!
I got only one comment:
could you please add to:
https://library.qiime2.org/plugins/

:pray:

Thank so much!
Luca

6 Likes

Hi @llenzi ,

I have just done it :+1:

6 Likes

This looks great @the_dummy!

One suggestion, you should add the original Krona reference to the plugin, so that the original authors get credit. Below are some examples from RESCRIPt:

Then you can test that it works by running qiime krona --citations.

5 Likes

Hi @SoilRotifer,

I wasn't sure how to cite it but your example helped me clarify my head. Thank you!

1 Like