Beta-Diversity export values

Is there a plugin like “make_distance_boxplots” in qiime1, so that I can get the values and calculate the significance between groups?
Also is there a way to export the pc values to plot in another program my PCoA?

Thank you for your help

Hah I just came here to ask the same question! I still use “make_distance_boxplots” from q1 to get aggregated distance values between samples. It’s especially helpful for when you want to compare within group distance to within group distance – the q2 beta significance plugin only appears to compare between group distances.

Hi there @cla & @vrbana! Have you had a chance to see this post from @colinbrislawn?

Take a look at that and let us know if it gets you moving in the right direction. Thanks! :t_rex: :qiime2:

I mean yeah you could just export the distance matrix and make your own boxplots, but this requires writing code to pull out the samples in different groupings, do within group distances and between group distances, and then running your own significance testing where Qiime 1 already does all of this. It would be awesome to have this same functionality in Qiime 2 since I am lazy :slight_smile:

From what I understand, the current beta significance plugin only allows you to compare between group distances (and doesn’t have an option to obtain the aggregated raw data, but it looks like its being added). I find comparing the within group distances is often very informative and really liked how Qiime 1 allowed you to look at this.

The qiime1 script you are referencing uses two-sample t-tests to compare these distributions.

This has not been re-implemented in QIIME 2 because, unfortunately, two-sample t-tests are not actually appropriate for comparing distance data (as far as I know), since distance measurements are not independent. So that qiime1 script is going to be prone to false positive errors (i.e., it will say your groups are significantly different when they are not).

For between-group distances, PERMANOVA and anosim (as used in QIIME 2) are preferred. For comparing within- vs. between-group distance distributions we do not yet have a good replacement in place (otherwise it would have been easy to reimplement the qiime1 methods in qiime2!). If you have any recommendations, we would be very pleased to hear :smile:

Thank you for your help.
I think the beta-group-significance plugin of qiime2 is great!
However, I would really appreciate if we get more options to export the results to generate plots that can be published.
Hence I am very interested to be able to download a csv file with the pc-values for PCoA plotting as well as the Permanova-results.


We have an open issue to expose the raw data with a download link in the visualization. Stay tuned!

That can be done. qiime diversity pcoa will produce PCoA results, which you input to, e.g., q2-emperor for plotting. You can also use qiime tools export to export those results to a text file if you want to examine individually.

Permanova results can be downloaded as a CSV from the visualization. Look for the “Download csv” link in the visualization.


I didn’t see that we can simply use the export the plugin to get the pc-values.
Thank you for pointing it out

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