#
# qtl.comparison.plot.R
#
# Copyright (c) 2010-2013 GBIC: Danny Arends, Konrad Zych and Ritsert C. Jansen
# last modified May, 2013
# first written Nov, 2012
# Contains: qtl.comparison.plot
#
# qtl.comparison.plot
#
# DESCRIPTION:
# function to create new map and save it in cross object
# PARAMETERS:
# - cross1 - object of class cross
# - cross2 - object of class cross
# - chr - which chromosome whoudl be plotted
# - ... - sent to scanone
# OUTPUT:
# An object of class cross
#
qtl.comparison.plot <- function(cross1, cross2, chr, ...){
if(missing(cross1)) stop("Provide two objects of class cross!\n")
if(missing(cross2)) stop("Provide two objects of class cross!\n")
if(!(any(class(cross1)=="cross"))) stop("Provide two objects of class cross!\n")
if(!(any(class(cross2)=="cross"))) stop("Provide two objects of class cross!\n")
res1 <- scanone(cross1,...)
res2 <- scanone(cross2,...)
if((missing(chr))){
chr <- 1
}
if(length(chr)>1){
chr <- chr[1]
warning("Function can plot only one chromosome at the time, plotting first of selected chromosomes!")
}
if(!(chr%in%1:min(nchr(cross1),nchr(cross2)))){
stop("Chromosome asked is not present in the cross object\n")
}
plot(res1,res2,col=c("orange","black"),chr=chr,main="Figure 2 - QTL profiles comparison.")
}
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