how to test_differential_abundance_Wilcoxon rank test (Wilcoxon rank sum differential abundance test) from phyloseq object?

Question

[MSRS]

Can anyone help in this issue

https://github.com/joey711/phyloseq/issues/1414

Can anyone please suggest how can I perform the differential abundance Wilcoxon rank test from the Phyloseq object (following tutorial: https://vaulot.github.io/tutorials/Phyloseq_tutorial.html). and from them, plotting "median relative abundance of genera (filled circles) and the interquartile range of the distribution (whiskers)" as an attached figure. and if possible convert the phyloseq object to indicspecies (https://cran.r-project.org/web/packages/indicspecies/index.html) to plot 2nd figure. Thank you

[Dunois]

That second plot is just a "regular" plot (and can be constructed, for example, as demonstrated in this post: https://www.biostars.org/p/463626/#464740).

[MSRS]

Thank you Dunois. Could you kindly share a demo of my desired figure (2)? I found little bit difference from your previous post. Thank you

[WouterDeCoster]

Please don't delete a question after someone spends the time to help you.

[MSRS]

Apology! Make sure to follow in future.

Answer 1

[MSRS]

Solution here

https://stackoverflow.com/questions/64842707/bubble-in-ggplot2-for-specific-dataframe#