krona: Make Krona files using KronaTools.

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Make Krona files using KronaTools.

Description

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()

Details

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

Value

A html file

Author(s)

Adrien Taudière

See Also

merge_krona

Examples

data("GlobalPatterns", package = "phyloseq")
GA <- subset_taxa(GlobalPatterns, Phylum == "Acidobacteria")
## Not run: 
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"))

## End(Not run)

MiscMetabar documentation built on Oct. 8, 2024, 1:07 a.m.