#' create_karyotype
#'
#' Generate karyotype file. run after initialising circos as it is dependent on variables declared within that function
#' The karyotype.txt file will be saved within the current working directory in a folder called data
#' @export
create_karyotype = function(){
m = 0
j = 1
k = 1
x = .Condition +1
sink("data/karyotype.txt")
for (i in 1:(((.Condition + 1) * .Comparison) + 1)){
e = (((.Condition + 1) * .Comparison) + 1)
if (((i+.Condition) %% x) == 0){
if (i == 1 || i == e){
cat(paste("chr", "-", paste("Blk.", j, sep=""), i, m, m + (.gap/2), "white\n", sep = "\t"))
m = m + (.gap/2)
j = j + 1
} else {
cat(paste("chr", "-", paste("Blk.", j, sep=""), i, m, m + .gap, "white\n", sep = "\t"))
m = m + .gap
j = j + 1
}
} else {
cat(paste("chr", "-", sheet_list[[k]], i, m, m + nrow(gene_list[[k]]), "black\n", sep = "\t"))
m = m + nrow(gene_list[[k]])
k = k + 1
}
}
sink(NULL)
}
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