Adding Taxonomic Ranks to Phyloseq?

[kbdilliplaine]

Hello, I am just found your package and am only now working my way through the available information.

Is there a way to correct phyloseq ranks when importing qiime2 .qza files? I use the PR2 database which has 9 taxonomic ranks starting at Domain, Supergroup etc. so not only are the ranks incorrect, but I am missing the genus and species entirely.

Thank you!

[david-barnett]

Hi,

Not sure what your specific aim is, but here are some suggestions and examples:

• If you just want to change the names of the ranks in the phyloseq, that is straightforward, see below
• Modifying and deleting the ranks you have available is also possible with tax_mutate(), see below
• If you need genus and species level classifications, but didn't obtain info for these ranks during your classification process, I think you will need to look again at your taxonomic classification process

library(phyloseq)
library(microViz)
#> microViz version 0.10.10 - Copyright (C) 2023 David Barnett
#> ! Website: https://david-barnett.github.io/microViz
#> ✔ Useful?  For citation details, run: `citation("microViz")`
#> ✖ Silence? `suppressPackageStartupMessages(library(microViz))`

# example phyloseq data
data("GlobalPatterns")
rank_names(GlobalPatterns)
#> [1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"

colnames(GlobalPatterns@tax_table)
#> [1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"

# example of setting new names
colnames(GlobalPatterns@tax_table) <- c("K.", "P.", "C.", "O.", "F.", "G.", "S.")
rank_names(GlobalPatterns)
#> [1] "K." "P." "C." "O." "F." "G." "S."

# example of modifying ranks with microViz tax_mutate
GP <- GlobalPatterns %>% tax_mutate(
    F_G = paste(F., G., sep = "_"), # combines 2 ranks
    F. = NULL, G. = NULL, S. = NULL # deletes these 3 ranks
)

rank_names(GP)
#> [1] "K."  "P."  "C."  "O."  "F_G"

GlobalPatterns@tax_table[30:40, 4:7]
#> Taxonomy Table:     [11 taxa by 4 taxonomic ranks]:
#>        O.              F.               G.               S.                    
#> 185612 "Cenarchaeales" "Cenarchaeaceae" NA               NA                    
#> 321018 "Cenarchaeales" "Cenarchaeaceae" NA               NA                    
#> 549041 "Cenarchaeales" "Cenarchaeaceae" "Cenarchaeum"    NA                    
#> 153762 "Cenarchaeales" "Cenarchaeaceae" "Cenarchaeum"    NA                    
#> 155789 "Cenarchaeales" "Cenarchaeaceae" "Cenarchaeum"    NA                    
#> 155495 "Cenarchaeales" "Cenarchaeaceae" "Cenarchaeum"    "Cenarchaeumsymbiosum"
#> 1029   "Cenarchaeales" "Cenarchaeaceae" "Cenarchaeum"    "Cenarchaeumsymbiosum"
#> 155526 "Cenarchaeales" "Cenarchaeaceae" "Nitrosopumilus" NA                    
#> 197473 "Cenarchaeales" "Cenarchaeaceae" "Nitrosopumilus" NA                    
#> 315545 "Cenarchaeales" "Cenarchaeaceae" "Nitrosopumilus" NA                    
#> 348549 "Cenarchaeales" "Cenarchaeaceae" "Nitrosopumilus" NA

GP@tax_table[30:40, 4:5]
#> Taxonomy Table:     [11 taxa by 2 taxonomic ranks]:
#>        O.              F_G                            
#> 185612 "Cenarchaeales" "Cenarchaeaceae_NA"            
#> 321018 "Cenarchaeales" "Cenarchaeaceae_NA"            
#> 549041 "Cenarchaeales" "Cenarchaeaceae_Cenarchaeum"   
#> 153762 "Cenarchaeales" "Cenarchaeaceae_Cenarchaeum"   
#> 155789 "Cenarchaeales" "Cenarchaeaceae_Cenarchaeum"   
#> 155495 "Cenarchaeales" "Cenarchaeaceae_Cenarchaeum"   
#> 1029   "Cenarchaeales" "Cenarchaeaceae_Cenarchaeum"   
#> 155526 "Cenarchaeales" "Cenarchaeaceae_Nitrosopumilus"
#> 197473 "Cenarchaeales" "Cenarchaeaceae_Nitrosopumilus"
#> 315545 "Cenarchaeales" "Cenarchaeaceae_Nitrosopumilus"
#> 348549 "Cenarchaeales" "Cenarchaeaceae_Nitrosopumilus"

^{Created on 2023-07-19 with reprex v2.0.2}

[kbdilliplaine]

Thank you! TLDR: qiime2R is the package responsible for handling the taxonomic ranks and modifying the code there solves the problem.

I did some digging this morning to locate where the taxonomy rank number and names come from during import from qiime2. qiime2R::parse_taxonomy() is responsible for handling this and is default set to the 7 taxonomic levels we learned as kids.

I was able to edit the function using trace("parse_taxonomy", edit=TRUE) to change the names of the taxonomic ranks and add the two that were missing. https://stackoverflow.com/questions/76717311/how-to-add-and-specify-additional-ranks-to-phyloseq-taxonomy for the full answer.