Creating 2D PCoA plots

[Nicholas_Bokulich]

Hi @dadaria ,
To add a few more solutions:

Exporting to R or Python:

PCoA plots with confidence ellipsoids

I need to render 2D PCoA plots with confidence ellipsoids. After going through help forum posts here I found others looking to do the same and roadmap plans from 2017 to add this functionality--it seemed that this had been added. I generated a jackknifed Emperor plot using "qiime diversity beta-rarefaction", which I had hoped would have confidence ellipsoids, but it did not, so I exported the data from this visualization.qzv file using "qiime tools export" and then tried to render the 2D plot us…

You can also directly view PCoAs using Vega to make 2D and customize:

Custom color palette

Hi @Parix! That depends on what visualization you're working with. Many visualizations (e.g. taxa barplot) have colorbrewer palettes baked in for you to use. Other visualizations may offer different approaches. (e.g. emperor plots allow editing in Vega - very powerful, but there's a bit of a learning curve) [image] Big-picture, it's important to remember that QIIME 2 uses a plugin-based model, where all bioinformatics knowledge is implemented in plugins, rather than in a sing…

A separate python package, dokdo:

Python Tutorial: Data Visualization with Dokdo API

This tutorial has gotten so big that apparently the text body exceeded the maximum number of characters one can enter in a post (99,000)! Therefore, I will leave a link to Dokdo API for those who are interested in seeing the most up-to-date tutorial. Please let me know if you have any questions. Click here to see the original documentation