Discussion about QIIME 2 Parkinson's mouse tutorial

My first question relates to the Parkinson’s mouse tutorial. How do you read an emperor plot and what are the different coordinates/axis? And how do you know what actually does have more beta diversity?

Hello Bethanie,

Great questions! Welcome to the forum! :qiime2:

The Parkinson’s Mouse Tutorial is one of the more advanced tutorials, and I think a good introduction to these concepts is in the Moving Pictures Tutorial: Alpha and Beta diversity analysis. This tutorial not only explains the concepts, but it also offers ‘discussion questions’ that show you what you could learn from a given graph.

Got to check out Moving Pictures! :movie_camera: :timer_clock:


If you are interested in an article, try this one:
Figure 7 has Emperor plots and shows exactly how to interpret them.
(This paper uses an older version of Qiime, so the Qiime-specific stuff is going to be different but the biology is going to be the same.)

Let us know if you have more questions!
Colin

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Hi Colin,

I’ve checked out the moving pictures tutorial, and the fmt one :slight_smile: but am finding the Parkinson’s mouse the most helpful. And thanks for the article!!
So I understand that I’m looking for clustering in the emperor plot, by different metadata columns, to see if there is a difference in diversity. But is there a way of quantifying which group has more diversity? Is one of the axis beta diversity? I know you can edit the axis to show time or other variables, but what are the original axes?
Hope this makes sense,

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It sounds like maybe you are thinking more in terms of alpha diversity here, which is not really related to the emperor visualizations… I recommend reading up more on alpha vs. beta diversity and the differences between these.

Alpha diversity is going to tell you how many species/phylotypes etc are in each sample, giving you a sense of “which group is more diverse”

Beta diversity is going to tell you how different those samples/groups are from one another. So higher beta diversity would be something like larger intra-group distance, which does not sound like what you are after. But maybe it is.

So quantify alpha diversity with qiime diversity alpha-group-significance and beta diversity with qiime diversity beta-group-significance

Here is a nice primer:

I hope that helps!

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Thank you so much!! I’m new to microbial ecology/statistics but the Gusta Me blog really helped!!

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