summarise_physeq: Summarize a phyloseq object
In simeross/CuPhyR: Custom Functions for Microbiome Analysis with Phyloseq

Description Usage Arguments Value Author(s) Examples

View source: R/summarise_physeq.R

Summarize the total number of ASVs, number of ASVs in a subset and percentage of reads this ASV subset contains (of total) of a given phyloseq object.

summarise_physeq(
  physeq = ps,
  ASV_sublist = c(),
  sublist_id = "sublist_id_not_defined",
  samp_names = TRUE
)

`physeq`	a phyloseq object to be summarized
`ASV_sublist`	a character vector of ASVs/OTUs (phyloseq taxa). Empty by default. If provided the summary will contain the percentage of abundance the sublist comprises. Compatible with cuphyr::list_subset_ASVs().
`sublist_id`	a character string describing the subset of taxa provided in ASV_sublist
`samp_names`	TRUE/FALSE. If TRUE (default), sample names in the subset are included in the summary.

a character string summarising the provided phyloseq object

Simeon Rossmann

summarise_physeq(ps)
summarise_physeq(ps, ASV_sublist= c("ASV1"), sublist_id ="ASV1", samp_names=FALSE)

phyt_ASVs <- cuphyr::list_subset_ASVs(physeq = ps, subv = c("Phytophthora","Phytopythium"), taxlvlsub="Genus")
summarise_physeq(ps, ASV_sublist= phyt_ASVs, sublist_id ="Phytophthora and Phytopythium", samp_names=FALSE)