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grunwaldlab / metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
http://grunwaldlab.github.io/metacoder_documentation
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Error in filter_taxa(x, per_taxon_max_change > 2.5, supertaxa = TRUE, : unused arguments #354

Closed Low-Maple closed 9 months ago

Low-Maple commented 9 months ago

Hi, Thank you for the metacoder package. I'm having an error while trying to run the code you added on Jan. 7, 2021 on issue #297. I have the error with hmp_otus and hm_samples data as well as with my own data. At the line :

x <- filter_taxa(x, per_taxon_max_change > 2.5, supertaxa = TRUE, reassign_obs = c(diff_table = FALSE))

I'm having the following error :

Error in filter_taxa(x, per_taxon_max_change > 2.5, supertaxa = TRUE, : unused arguments (supertaxa = TRUE, reassign_obs = c(diff_table = FALSE))

The resulting heat tree has the taxa that should have been filtered. It worked two days ago, so I'm not sure if I'm the one who did something wrong...

Thank you very much in advance.

zachary-foster commented 9 months ago

Do you have the phyloseq package loaded as well? That package also has a filter_taxa function and if you load it after metacoder you will be using the wrong function by mistake.

Low-Maple commented 9 months ago

You are right, I had the phyloseq package loaded. It works with metacoder::filter_taxa or by removing the phyloseq package. Thank you so much for your help.

Best,

zachary-foster commented 9 months ago

No problem!