How to plot a dendrogram in ampvis2?

[LingTJ]

Hello, dear ampvis2 developers, I have been using this package for several years, and cited this package in my paper (https://doi.org/10.1021/acs.jafc.2c01005). This is a good package for me. Now I'm trying to plot a dendrogram using both dissimilarity (Bray) and transform functions (Hellinger) for the PCoA. But I could not find the codes/functions in home page of ampvis2. Could you pleae tell me how to do this in ampvis2? Thank you.

TJ Ling

Thank you for using ampvis2!

If you encounter a problem with ampvis2 that you are unable to resolve, this is the place for discussing the problem with developers to find a solution. To best help you quickly, please first make sure that:

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• you have carefully read the documentation of the ampvis2 function(s) used
• you have searched the GitHub issues page or the internet for similar or identical problems

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[KasperSkytte]

Hi there. I have no plans to implement new features for a while, unless people contribute. But I'm not sure what you mean by adding dendrograms to an ordination plot, can you provide an example? But maybe this is equivalent https://rdrr.io/github/jfq3/ggordiplots/man/gg_ordicluster.html

[LingTJ]

Hi, Kasper, Thank you again for your quick reply. I have addressed the issue by using packages of vegan and factoextra. The key functions are decostand in vegan, which is able to do transform (Hellinger) before Bray-Curtis distance algorithm. Thank you. TJ