change otu.table() sequence header to numbered OTUs with taxonomy

[RJ333]

Hello everyone,

I recently got into dada2 and phyloseq using this workflow: https://f1000research.com/articles/5-1492/v2
I followed it until all prepared data was combined into a phyloseq object. I provided an example with data from the mentioned article at stackoverflow:

https://stackoverflow.com/questions/53032504/combine-otu-and-tax-table-and-replace-actual-sequences-with-otu-ids-phyloseq-da

Now I'm wondering how I may get an otu.table(ps), that does not have the actual sequences as headers? I would like to combine the information from the taxonomy table and from the OTU table.
but so far no one could help and I thought this might be a more appropriate place to ask for help. I try to create a format as this:

        full_taxonomy_OTU00001  full_taxonomy_OTU00002   full_taxonomy_OTU00003
F3D0    counts                  counts                  counts
F3D1    counts                  counts                  counts
F3D11   counts                  counts                  counts
F3D125  counts                  counts                  counts

I assume I'm just not finding an obvious function for this? I've looked around quite a bit but couldn't find something specific that was helpful.

Thank you very much

René

[jjrahn]

I am having the same problem. The OTUs are labeled as the full sequence which makes doing any plots that utilize the OTU names impossible for the computer to display.

[spholmes]

Normally we use the assignTaxonomy workflow to provide the taxonomic names. Then you can choose to change the names in the otu_table using this: https://benjjneb.github.io/dada2/assign.html The species information should be transferred into the taxa_names object and taxa_table. Usually we just give the otus short names (keeping the sequence information safely elsewhere for data combining). taxa_names(psobject) <- paste0("Seq", seq(ntaxa(psobject))) A very long discussion of more intricate ways of doing this appears here: #213 Hope this helps,

…

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[RJ333]

Thank you for your comment and apologies for the late reply. I crosslinked this post to my question on stackoverflow.com. But I'm still unable to add the taxonomy within the header (which is now Seq_001, Seq_002 etc). I'll try to find a way for that.

René

[RJ333]

I think a found a (still dirty looking) way to achieve my goal. I will show the code here, more is explained on

https://stackoverflow.com/questions/53032504/combine-otu-and-tax-table-and-replace-actual-sequences-with-otu-ids-phyloseq-da

# this changes the header from the actual sequence to Seq_001, Seq_002 etc
taxa_names(ps)
n_seqs <- seq(ntaxa(ps))
len_n_seqs <- nchar(max(n_seqs))
taxa_names(ps) <- paste("Seq", formatC(n_seqs, 
                                            width = len_n_seqs, 
                                            flag = "0"), sep = "_")
taxa_names(ps)

A possible way to get taxonomy included into the header is the following (continuing from above):

# generate a vector containing the full taxonomy path for all OTUs
wholetax <- do.call(paste, c(as.data.frame(tax_table(ps))
                  [c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus")], 
                  sep = "__"))  # to distinguish from "_" within tax ranks

# turn the otu_table into a data.frame
otu_export <- as.data.frame(otu_table(ps))
tmp <- names(otu_export)

# paste wholetax and OTU_ids together
for(i in 1:length(tmp)){
names(tmp)[i] = paste(wholetax[i], tmp[i], sep = "__")
}

# overwrite old names
names(otu_export) <- names(tmp)

> head(otu_export)[5]

# output:  
     Bacteria__Bacteroidetes__Bacteroidia__Bacteroidales__Bacteroidaceae__Bacteroides__Seq_005
F3D0                                                                                         146
F3D1                                                                                         126
F3D11                                                                                        496
F3D125                                                                                       440
F3D13                                                                                       1183
F3D141                                                                                       184

maybe it is possible to include a function that performs the above in a clean way, within the phyloseq-structure? It might also be possible to provide the wholetaxvector to the taxa_names() command, but I haven't tested that and I'm not sure whether this is desirable for further downstream analysis?