Paul J. McMurdie

I couldn't see package information, etc., but I'll update dependency requirements very soon, basically as soon as the BioC release happens later today...

Also, I can't "see" your attachment. Where is your MRE?

Please go here for posting and you'll understand why I can't see it... https://github.com/joey711/shiny-phyloseq/issues/65 please post a URL, code, instructions, etc...

I'll add this very soon...

Thanks @spholmes ! Actually, ellipses are finally _natively_ supported in ggplot2, so I was simply going to add an ellipse layer. I think it takes function inputs as alternative ellipse...

This can be fixed by (1) including a default `set.seed` argument to the top-level wrapping functions that sometimes utilize a random process. `plot_net` is the top among them. `plot_heatmap` and...

Solved for `plot_net`. Needs to be fixed as well for heatmap and ordination...

@sentausa , @michberr is correct. you do not have any sample variables in your data object. Did you expect otherwise? Since you haven't provided a MRE, there's no further debugging...

you make a good point :)

The quick answer to your issue title/description is that the following works and keeps the index names: ```R physeq %>% tax_table() %>% as("matrix") %>% data.frame() %>% head ``` `taxonomyTable` class...