Most abundant genera across a complete phyloseq object

[slambrechts]

Hi,

I'm trying to use fantaxtic to get the top 10 most abundant genera across a complete phyloseq object and list the relative abundances of these top genera. I was trying to do this like so:

top <- top_taxa(physeq, 
                tax_level = "Genus", 
                n_taxa = 10)

But I get:

Error in dimnames(x) <- dn : 
  length of 'dimnames' [1] not equal to array extent

Maybe this has something to do with the fact that I classified my OTUs using Lotus2, and therefore there are "?" in my tax table?

[gmteunisse]

Question marks should definitely be replaced with NA values. Another thing to check is that the tax_table has the correct order (col_1=kingdom, …, col_n=species). If that doesn’t solve it, could you post a reproducible example with data?

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From: Sam Lambrechts @.> Sent: Tuesday, December 12, 2023 11:21:12 AM To: gmteunisse/fantaxtic @.> Cc: Subscribed @.***> Subject: [gmteunisse/fantaxtic] Most abundant genera across a complete phyloseq object (Issue #26)

Hi,

I'm trying to use fantaxtic to get the top 10 most abundant genera across a complete phyloseq object and list the relative abundances of these top genera. I was trying to do this like so:

top <- top_taxa(physeq, tax_level = "Genus", n_taxa = 10)

But I get:

Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent

Maybe this has something to do with the fact that I classified my OTUs using Lotus2, and therefore there are "?" in my tax table?

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[slambrechts]

Thank you for the info

col_1 is listed as Domain instead of kingdom at the moment

I will first replace question marks with NA values

[gmteunisse]

Has your issue been resolved?

[slambrechts]

Hi, no the problem remained after the modifications, so I ended up using something else

[gmteunisse]

I'm sad to hear that. Could you post a reproducible example? It would be nice if I can see what the problem is and fix it.