Copy phyloseq otu_table data to sample_data

Copy phyloseq otu_table data to sample_data

ps_otu2samdat(ps, taxa = NULL)

Arguments

ps

phyloseq with sample_data

taxa

list of taxa_names to copy to sample_data, or NULL (which selects all with phyloseq::taxa_names())

Value

phyloseq with augmented sample_data

Examples

library(phyloseq)
data("dietswap", package = "microbiome")

ps <- dietswap %>% ps_otu2samdat("Akkermansia")
sample_variables(ps)
#> [1] "subject"                "sex"                    "nationality"           
#> [4] "group"                  "sample"                 "timepoint"             
#> [7] "timepoint.within.group" "bmi_group"              "Akkermansia"           

# or if you do not specify any taxa, all are copied
ps_all <- dietswap %>% ps_otu2samdat()
sample_variables(ps_all)[1:15]
#>  [1] "subject"                      "sex"                         
#>  [3] "nationality"                  "group"                       
#>  [5] "sample"                       "timepoint"                   
#>  [7] "timepoint.within.group"       "bmi_group"                   
#>  [9] "Actinomycetaceae"             "Aerococcus"                  
#> [11] "Aeromonas"                    "Akkermansia"                 
#> [13] "Alcaligenes faecalis et rel." "Allistipes et rel."          
#> [15] "Anaerobiospirillum"          

# this could be useful for colouring ordination plots, for example
ps %>%
  ps_mutate(log_akkermansia = log(Akkermansia)) %>%
  dist_calc("bray") %>%
  ord_calc(method = "PCoA") %>%
  ord_plot(
    colour = "log_akkermansia",
    size = 3, shape = "nationality"
  )