R/shortenCladeName.R

In lwaldron/LeviRmisc: Levi's miscellaneous handy R functions

shortenCladeName <- function #Shorten Maaslin-compliant or QIIME-compliant taxonomical clade names
### Keeps only the last informative bit (containing a __, plus taxid
### integer if present), for nicer plotting.
### Function by Levi Waldron.
(x,
### A vector of QIIME taxonomic names, pipe-separated.
 separator="|"
### The character used to separate levels of the taxonomy: ";" for QIIME, "|" for Maaslin.
 ){
    split.names <- strsplit(x, separator, fixed=TRUE)
    sapply(1:length(split.names), function(i){
        if (sum(grepl("__", split.names[[i]])) == 0){
            return(x[i])
        }else{
             return(paste(split.names[[i]][max(grep("__", split.names[[i]])):length(split.names[[i]])], collapse="|"))
        }})
### a vector the same length as x, providing only the leaf-level
### names of the taxonomy.
}