comp_barplot with OTU/ASV?

[lxsteiner]

Hi,

How to make comp_barplot work on the lowest level (OTU/ASV)? Because not specifying tax_level throws an error:

  argument "tax_level" is missing, with no default

since this level doesn't exist in rank_names of a phyloseq object.

Thanks!

[david-barnett]

Hi, simplest way is to set tax_level as "unique"

Better ways involve using tax_names2rank, which creates a new rank (with any rank name you like) from the taxa names - see some examples below

(note to self: this should be better documented)

library(microViz)
#> microViz version 0.12.6 - Copyright (C) 2021-2024 David Barnett
#> ! Website: https://david-barnett.github.io/microViz
#> ✔ Useful?  For citation details, run: `citation("microViz")`
#> ✖ Silence? `suppressPackageStartupMessages(library(microViz))`

microViz::ibd %>%
  ps_filter(gender == "female") %>% 
  tax_fix() %>% 
  comp_barplot(tax_level = "unique")
#> Registered S3 method overwritten by 'seriation':
#>   method         from 
#>   reorder.hclust vegan

microViz::ibd %>%
  ps_filter(gender == "female") %>% 
  tax_fix() %>% 
  tax_names2rank("O.T.U.") %>% 
  comp_barplot(tax_level = "O.T.U.")

microViz::ibd %>%
  ps_filter(gender == "female") %>% 
  tax_fix() %>% 
  tax_rename(rank = "Genus", pad_digits = 2) %>% 
  tax_names2rank("O.T.U.") %>% 
  comp_barplot(tax_level = "O.T.U.")

  
microViz::ibd %>%
  tax_filter(min_prevalence = 2) %>% # remove singletons
  ps_filter(gender == "female") %>% 
  tax_fix() %>% 
  tax_rename(rank = "Genus", pad_digits = 2) %>% 
  tax_names2rank("O.T.U.") %>% 
  comp_barplot(tax_level = "O.T.U.", merge_other = FALSE)

^{Created on 2024-12-16 with reprex v2.1.1}