R/num_pheno.R

In byandell/qtl2shiny: Shiny interface for 'qtl2' Fine Mapping

# Number of phenotypes examined
#
# Character string with number of phenotypes of total.
num_pheno <- function(pheno, analyses_tbl) {
  if(any(c("all","none") %in% pheno))
    return(NULL)
  
  hr_num <- function(x, digits_ct=0) {
    x <- gdata::humanReadable(x, digits=digits_ct, sep="",
                              standard="SI",
                              justify=c("right","right"))
    substring(x, 1, nchar(x) - 1)
  }
  
  num_pheno <- length(unique(pheno))
  if(!num_pheno || is.null(analyses_tbl))
    return(NULL)
  tot_pheno <- nrow(dplyr::distinct(analyses_tbl, pheno, .keep_all=TRUE))
  ## Put in human-readable format
  num_pheno <- hr_num(num_pheno, 0)
  tot_pheno <- hr_num(tot_pheno, 2)
  paste("Phenotypes:", num_pheno, "of", tot_pheno)
}