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biocore / emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets
http://biocore.github.io/emperor/
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How to draw a 95% confidence ellipse in a Emperor PCoA? #807

Closed oseias-r-junior closed 2 years ago

oseias-r-junior commented 2 years ago

Hello, Is that possible to draw a 95% confidence ellipse around the dots representing a set of samples in Emperor? I saw some related issues, but it seems also that it stopped being updated a long ago. So, IDK if there is already something new regarding this topic.

If so, is there an example/pipeline that someone can follow on how to include it in a given PCoA made in Emperor? Thanks in advance!

antgonza commented 2 years ago

You are looking for https://docs.qiime2.org/2021.11/plugins/available/diversity/beta-rarefaction/.

oseias-r-junior commented 2 years ago

Sorry, saw that you closed the issue, but your answer hasn't actually solved my question.

I mean a 95 % confidence interval in a 3D PCoA (like here), also, I was thinking of an example for a jupyter notebook? BTW, the link you sent seems to be outdated or not supported anymore.

ElDeveloper commented 2 years ago

If you have a set of ordinations for which you would like to draw ellipses around a reference ordination. You can use the jackknifing API as shown in this notebook: https://nbviewer.org/github/biocore/emperor/blob/new-api/examples/jackknifed.ipynb

Through the notebook API you can select different methods to draw these ellipses i.e. IQR for interquartile range, ideal_fourths for quartiles based on the ideal fourths method, and sdev for standard deviation.

The document @antgonza linked to, shows the QIIME2 pipeline to compute ellipses for ordinations resulting from multiple rarefactions at the same sequencing depth. Here's the latest version of this URL: https://docs.qiime2.org/2022.2/plugins/available/diversity/beta-rarefaction/