#' Modify lineage names from sequence alignment so they match names in database
#' @importFrom dplyr mutate
#' @importFrom dplyr recode
#' @importFrom dplyr rename
#' @importFrom dplyr select
#' @importFrom magrittr %>%
#' @export
clean_names <- function(lin.names, keep.genus = FALSE){
X1=X2=parasiteGenus=NULL
out <- data.frame(do.call("rbind", strsplit(as.character(lin.names), "_")))
if(keep.genus == FALSE){
return(as.character(out[,2]))
} else{
out.n <- out %>%
select(X1, X2) %>%
rename(parasiteGenus = X1, Lineage_Name = X2) %>%
mutate(parasiteGenus = recode(parasiteGenus,
P = "Plasmodium",
H = "Haemoproteus",
L = "Leucocytozoon"))
return(out.n)
}
}
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