Getting NA's for taxon_ranks

[ThaisaJungles]

metacode.zip

I'm getting only NA's in my taxon ranks after running parse_tax_data. I tried a couple of things for the regex, but still could not get it to work. Any ideas? Attached are my files and this is the code I'm using:

meta <-read_csv("metadata_metacode.csv") table<-read_csv("table_metacode.csv")

obj <- parse_tax_data(table, class_cols = "lineage", # the column that contains taxonomic information class_sep = ";", # The character used to separate taxa in the classification class_regex = "^(.+)__(.*)$", # Regex identifying where the data for each taxon is class_key = c(tax_rank = "info", # A key describing each regex capture group tax_name = "taxon_name"))

[zachary-foster]

Thanks for including input data and code!

That is because you need to use tax_rank = "taxon_rank" instead of tax_rank = "info" so that the function knows those are taxon ranks instead of some other type of arbitrary per-taxon info.

library(readr)
library(metacoder)

meta <-read_csv("~/Downloads/metadata_metacode.csv")
table<-read_csv("~/Downloads/table_metacode.csv")

obj <- parse_tax_data(table,
                      class_cols = "lineage", # the column that contains taxonomic information
                      class_sep = ";", # The character used to separate taxa in the classification
                      class_regex = "^(.+)__(.*)$", # Regex identifying where the data for each taxon is
                      class_key = c(tax_rank = "taxon_rank", # A key describing each regex capture group
                                    tax_name = "taxon_name"))
head(taxon_ranks(obj))
#>  ab  ac  ad  ae  af  ag 
#> "r" "p" "p" "p" "p" "p"

^{Created on 2021-04-13 by the reprex package (v0.3.0)}

That example you copied from was written before that was a feature. I will update it.

[ThaisaJungles]

Many thanks, it worked great! One last question not related to it, but is there a way to make the node's size get bigger as the relative abundance increases instead of the number of OTUs?

[zachary-foster]

Yes, you need to replace n_obs with the name of the column storing per-taxon relative abundance or some other variable storing that information. You can calculate per-taxon relative abundance with calc_taxon_abund. The plots on this page give an example of the idea:

https://grunwaldlab.github.io/metacoder_documentation/example.html

you can plot any per-taxon value for either color or size.