Description Usage Arguments Value
Given a phyloseq object (with absolute abundance counts) and a taxonomic rank (character - one among 'rank_names(physeq)') it gives the taxa (by 'tax_rank') summarized for the whole data set ranked by abundance.
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physeq |
phyloseq-class object. |
tax_rank |
taxonomic rank (character). One of the taxonomic ranks among the column names of 'tax_table()' of the 'physeq' object given. |
count_type |
type of counts to perform 'rank_taxa()'. It can be absolute, i.e., 'abs', or percentage, i.e., 'perc' (character). Default is 'abs' - absolute counts. |
top_taxa |
top most abundant taxa to select by 'tax_rank' (numeric - coerced to integer) in the overall data set. Default 'NULL'. If 'count_type = perc', the percentage ranging from 0-100% will be determined for the 'top_taxa' only. |
show_top |
top n taxa to show (numeric - coerced to integer). Default is 'NULL'. The difference to 'top_taxa' is that if 'count_type = "perc"', the percentage presented still refers to the percentage of overall data before discarding the non-top n taxa. |
group |
factorial variable to group, one among 'sample_variables(physeq)'. Default is 'NULL'. |
taxa_perc_cutoff |
percentage cutoff to remove less abundant taxa than 'taxa_perc_cutoff'. Default is 'NULL'. |
rm_na |
include (TRUE) or not (FALSE) NAs, i.e., taxa without classification at the taxonomic level specified at 'tax_rank'. |
... |
parameters to be passed to the function 'filter_feature_table()'. |
It returns a list with a tibble data frame ('$data') and ggplot ('$plot') ranking the taxa picked at the taxonomic rank select at 'tax_rank'.
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