R/ctl.hist.R

In ctl: Correlated Trait Locus Mapping

#
# ctl.hist.R
#
# copyright (c) 2010-2012 - GBIC, Danny Arends, Bruno Tesson and Ritsert C. Jansen
# last modified Oct, 2012
# first written Dec, 2011
# 
# Histogram routines for CTL analysis

hist.CTLobject <- function(x, phenocol = 1, ...) {
  if(missing(x)) stop("argument 'x' which expects a 'CTLobject' object is missing, with no default")
  namez <- NULL
  plot(c(0, 1.0), c(0, length(unlist(x[[phenocol[1]]]$perms))/5), type='n', main = "CTL scores permutations", ylab = "Frequency", xlab = "Difference in correlation^2")
  for(pheno in phenocol) {
    if(is.null(x[[pheno]]$perms)) stop(paste("Permutations not found for phenocol=", pheno))
    sorted <- sort(unlist(x[[pheno]]$perms))
    hist(sorted, breaks = seq(0,1.0,0.01), add = TRUE, col = pheno, ...)
    namez <- c(namez,ctl.name(x[[pheno]]))
  }
  legend("topright", legend = namez, col = phenocol, lwd = 6)
}

# end of ctl.hist.R