Make Krona files using KronaTools.

Need the installation of kronatools on the computer (installation instruction).

Usage

krona(
  physeq,
  file = "krona.html",
  nb_seq = TRUE,
  ranks = "All",
  add_unassigned_rank = 0,
  name = NULL
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

file

(required) the location of the html file to save

nb_seq

(logical) If true, Krona set the distribution of sequences in the taxonomy. If False, Krona set the distribution of ASVs in the taxonomy.

ranks

Number of the taxonomic ranks to plot (num of the column in tax_table slot of your physeq object). Default setting plot all the ranks (argument 'All').

add_unassigned_rank

(int) Add unassigned for rank inferior to 'add_unassigned_rank' when necessary.

name

A name for intermediary files, Useful to name your krona result files before merging using merge_krona()

Value

A html file

Details

This function is mainly a wrapper of the work of others. Please cite Krona if you use this function.

See also

merge_krona

Author

Adrien Taudière

Examples

data("GlobalPatterns", package = "phyloseq")
GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘RNeXML’ ‘tidytree’
if (FALSE) { # \dontrun{
krona(GA, "Number.of.sequences.html")
krona(GA, "Number.of.ASVs.html", nb_seq = FALSE)
merge_krona(c("Number.of.sequences.html", "Number.of.ASVs.html"))
} # }