R/amp_rename.R

In MadsAlbertsen/ampvis: Tools for visualising amplicon data

#' Used for cleaning and renaming taxonomy in phyloseq objects
#'
#' Used internally in other ampvis functions.
#'
#' @usage amp_rename(data)
#'
#' @param data (required) A ampvis formated list with all data.
#' @param tax.class Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
#' @param tax.empty Either "remove" OTUs without taxonomic information at X level, with "best" classification or add the "OTU" name (default: best).
#' @param tax.level The taxonomic level to remove OTUs with empty taxonomy, only used when tax.empty = "remove" (default: Genus).
#' 
#' @return A phyloseq object with cleaned and renamed taxonomy.
#' 
#' @export
#' @import phyloseq
#' @import dplyr
#' 
#' @author Mads Albertsen \email{MadsAlbertsen85@@gmail.com}

amp_rename <- function(data, tax.class = NULL, tax.empty = "best", tax.level = "Genus"){
  
  tax <- data[["tax"]]
    
  ## First make sure that all entires are strings
  for ( i in 1:ncol(tax) ){
    tax[,i] <- as.character(tax[,i])  
  }
  
  ## Change a specific phylum to class level
  if(!is.null(tax.class)){
    for (i in 1:nrow(tax)){
      if (!is.na(tax$Phylum[i]) & tax$Phylum[i] %in% tax.class){
        tax$Phylum[i] <- tax$Class[i]   
      }
    }
  }
  
  ## Remove the underscore classifier from the data  
  tax$Kingdom <- gsub("k__", "", tax$Kingdom)
  tax$Phylum <- gsub("p__", "", tax$Phylum)
  tax$Phylum <- gsub("c__", "", tax$Phylum)
  tax$Class <- gsub("c__", "", tax$Class)
  tax$Order <- gsub("o__", "", tax$Order)
  tax$Family <- gsub("f__", "", tax$Family)
  tax$Genus <- gsub("g__", "", tax$Genus)
  tax$Kingdom <- gsub("uncultured", "", tax$Kingdom)
  tax$Phylum <- gsub("uncultured", "", tax$Phylum)
  tax$Phylum <- gsub("uncultured", "", tax$Phylum)
  tax$Class <- gsub("uncultured", "", tax$Class)
  tax$Order <- gsub("uncultured", "", tax$Order)
  tax$Family <- gsub("uncultured", "", tax$Family)
  tax$Genus <- gsub("uncultured", "", tax$Genus)
  
  ## Check if there is a species level otherwise add it for consistency
  if (!is.null(tax$Species)){
    tax$Species <- gsub("s__", "", tax$Species)
  } else {
    tax$Species <- ""
  }
  
  tax[is.na(tax)] <- ""
    
  ## How to handle empty taxonomic assignments
  if (tax.empty == "OTU"){
    for (i in 1:nrow(tax)) {
      if (tax[i,"Species"] == "") {tax[i,"Species"] <- rownames(tax)[i]}
      if (tax[i,"Genus"] == "") {tax[i,"Genus"] <- rownames(tax)[i]}
      if (tax[i,"Family"] == "") {tax[i,"Family"] <- rownames(tax)[i]}
      if (tax[i,"Order"] == "") {tax[i,"Order"] <- rownames(tax)[i]}
      if (tax[i,"Class"] == "") {tax[i,"Class"] <- rownames(tax)[i]}
      if (tax[i,"Phylum"] == "") {tax[i,"Phylum"] <- rownames(tax)[i]}
    }
  }
  
## Handle empty taxonomic strings
  if(tax.empty == "best"){
    tax <- mutate(tax, Kingdom, Kingdom = ifelse(Kingdom == "", "Unclassified", Kingdom)) %>%
      mutate(Phylum, Phylum = ifelse(Phylum == "", paste("k__", Kingdom, "_", rownames(tax), sep = ""), Phylum)) %>%
      mutate(Class, Class = ifelse(Class == "", ifelse(grepl("__", Phylum), Phylum, paste("c__", Phylum, "_", rownames(tax), sep = "")), Class)) %>%
      mutate(Order, Order = ifelse(Order == "", ifelse(grepl("__", Class), Class, paste("c__", Class, "_", rownames(tax), sep = "")), Order)) %>%
      mutate(Family, Family = ifelse(Family == "", ifelse(grepl("__", Order), Order, paste("o__", Order, "_", rownames(tax), sep = "")), Family)) %>%
      mutate(Genus, Genus = ifelse(Genus == "", ifelse(grepl("__", Family), Family, paste("f__", Family, "_", rownames(tax), sep = "")), Genus)) %>%
      mutate(Species, Species = ifelse(Species == "", ifelse(grepl("__", Genus), Genus, paste("g__", Genus, "_", rownames(tax), sep = "")), Species))
  }

  if(tax.empty == "remove"){
    abund <- data[["abund"]]
    tax <- subset(tax, tax[,tax.level] != "")
    abund <- subset(abund, rownames(abund) %in% rownames(tax))
    data[["abund"]] <- abund
  }
  data[["tax"]] <- tax
  
  return(data)
}