Top taxa in each individual sample

[pauGuas]

Hi, I need to see what are the top taxa in each individual sample. Is there a way to do that using fantaxtic? I can only see the top taxa across all samples in the entire phyloseq object.

[gmteunisse]

Hi pauGaus,

There is no such option in Fantaxtic, but I've written you some code to do so - see below. I might implement this into the package at some point, but for now, just copy and run the functions below.

Hope that this solves your issue!

require("phyloseq")
require("fantaxtic")
require("tidyverse")

# This function gets the top n taxa for every sample in a phyloseq object
get_top_sample_taxa <- function(ps_obj, n_taxa = 1){

  # Make sure taxa are rows
  if (!phyloseq::taxa_are_rows(ps_obj)) {
    otu_table(ps_obj) <- t(otu_tbl)
  }

  # Get the top taxa per sample
  top_taxa <- otu_table(ps_obj) %>% 
    data.frame(taxid = row.names(.)) %>% 
    pivot_longer(!taxid, names_to = "sample_id", values_to = "abundance") %>% 
    group_by(sample_id) %>% 
    slice_max(abundance, n = n_taxa) %>%
    arrange(desc(abundance)) %>%
    mutate(tax_rank = rank(x = -abundance, ties.method = "first", na.last = T))

  # Add taxonomic annotations
  top_taxa <- ps_obj %>%
    tax_table() %>%
    data.frame(taxid = row.names(.)) %>%
    right_join(top_taxa, by = "taxid")

  # Add relative abundance
  top_taxa <- ps_obj %>%
    sample_sums() %>%
    data.frame(sample_id = names(.),
               library_size = .) %>%
    right_join(top_taxa, by = "sample_id") %>%
    rowwise() %>%
    mutate(proportion = abundance / library_size)

  # Reorder
  top_taxa <- top_taxa %>%
    select(!library_size) %>%
    relocate(sample_id, tax_rank, taxid, abundance, proportion)

  return(top_taxa)
}

# This function merges all taxa that are not specified in 'taxa' into  a taxon 
# named 'other_label' if 'discard_other = FALSE', else it removes them.
collapse_taxa <- function(ps_obj, taxa, discard_other = FALSE, other_label = "Other"){

  # Make sure taxa are rows
  if (!phyloseq::taxa_are_rows(ps_obj)) {
    otu_table(ps_obj) <- t(otu_table(ps_obj)
  }

  # Merge or discard all other taxa
  if (discard_other) {
    ps_obj <- phyloseq::prune_taxa(taxa, ps_obj)
  } else {

    # Merge taxa
    to_merge <- phyloseq::taxa_names(ps_obj)
    to_merge <- to_merge[!(to_merge %in% taxa)]
    ps_obj <- merge_taxa(ps_obj, to_merge)

    # Update the taxon name to other_label
    tax_tbl <- phyloseq::tax_table(ps_obj)
    indx <- which(row.names(tax_tbl) %in% to_merge)
    tax_tbl[indx, ] <- other_label
    phyloseq::tax_table(ps_obj) <- tax_tbl
  }
  return(ps_obj)
}

# Load data
data(GlobalPatterns)
ps_obj <- GlobalPatterns

# Get the top n taxa per sample
top_taxa <- get_top_sample_taxa(ps_obj, n_taxa = 3)
top_taxa

### If you want to plot with fantaxtic, run the steps below ###

# Collapse taxa
ps_obj <- collapse_taxa(ps_obj, top_taxa$taxid)

# Generate labels
ps_obj <- name_taxa(ps_obj, label = "Unkown", species = T, other_label = "Other")

# Plot
fantaxtic_bar(ps_obj, color_by = "Phylum", label_by = "Species", other_label = "Other")

[gmteunisse]

Let me know if this was useful.

[pauGuas]

Thank you so much for sending this code. I actually found some other code that worked before you sent this, so I decided not to risk confusing myself by trying yours! Thank you.

[gmteunisse]

I'm glad to hear that you found a solution to your problem. Would you mind trying out the code above to see if it does what you want? I'd like to implement it into the package, but before I do so, any feedback would be appreciated.

[gmteunisse]

This issue has now been resolved. To get the top taxa per sample, run:

data(GlobalPatterns)
top <- top_taxa(GlobalPatterns, n_taxa = 1, grouping = "sample_id")