microViz
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david-barnett
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
Hello, and thank you for an excellent package! I was wondering if you had any documentation for interpretation of the taxatrees? I find it a bit difficult to be sure...
With many hundreds of ASVs and hundreds of samples, interactively selecting the unifrac distance options and clicking build appears to hang indefinitely because there is no indication to the user...
If during complex taxonomy table repairs, you want to replace unknowns, but not empty strings you cannot currently do this with tax fix The solution is probably to use NAchar...
`ps %>% tax_mutate(across(everything(), ~ gsub("^.__uncultured_.+$", "", .))) %>% tax_fix()` example thanks to Valentina
seriate samples with distance matrix that already exists in psExtra can also be used inside ps_seriate (for when distance is required for method) returns psExtra
and names in this sort order should be accessible via tax_top_ord (a sister function to tax_top)?
Hi @david-barnett, Thanks again for your effort in developping the package. How would you recommend to run mixed models thourgh `taxatree_models`? Following your [tutorial](https://david-barnett.github.io/microViz/articles/web-only/modelling-taxa.html), I am not able specify type...
Hi David, Thanks for developing and maintaining MicroViz, what a wonderful tool. I would like to suggest changing the error message for this issue: _@david-barnett in https://github.com/david-barnett/microViz/issues/53#issuecomment-1162229318_. I wanted to...
Hello first, thank you for this impressive suite of tools! I am trying to clean up my set of gut microbiome data. this includes multiple subjects and multiple tissues For...
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R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.