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contrasting.rainbow <- function (x, ...) {
x <- as.integer(x)[1]
stopifnot(x >= 1)
## make pretty colour cycle, by...
## ...finding non-unit divisors of ler...
xnud <- setdiff(which(x %% 1:x == 0), 1)
## ...and thus largest coprime of x that is <=x/2...
xcop <- max(which(sapply(1:(x/2), function(div) all(div %% xnud != 0))))
## ...and thus constrasting traversal of x
xtrav <- (1:x*xcop) %% x + 1
## fallback; no coprime exists so use random shuffle
if (!all(1:x %in% xtrav)) xtrav <- sample(x)
return(rainbow(x, ...)[xtrav])
}
## plotpos.by.chr <- function (chr, pos, gap = 5e7, chrset = c(1:22, "X", "Y", "M")) {
## stopifnot(length(pos) == length(chr))
## chr <- toupper(as.character(chr))
## chrset <- toupper(as.character(chrset))
## plotpos <- rep(NA, length(pos))
## ox <- 0
## for (cx in chrset) {
## this <- which(chr == cx | chr == paste("CHR", cx, sep = ""))
## plotpos[this] <- pos[this] - min(pos[this], na.rm = TRUE) + ox + gap
## ox <- max(plotpos[this], na.rm = TRUE)
## }
## return(plotpos)
## }
## plotcol.by.chr <- function (chr, cols = NULL, chrset = c(1:22, "X", "Y", "M")) {
## chrset <- toupper(as.character(chrset))
## chrnum <- match(sub("^CHR", "", toupper(as.character(chr))), chrset)
## if (is.null(cols)) {
## cdiv <- which.min(abs(length(chrset) %% (1:length(chrset)) - length(chrset)/3))
## cols <- rainbow(length(chrset))[(1:length(chrset) * cdiv) %% length(chrset) + 1]
## }
## return(rep(cols, length.out = length(chrset))[chrnum])
## }
## mid.by.chr <- function (chr, plotpos) {
## minpos <- rep(NA, 22)
## medpt <- rep(NA, 22)
## maxpos <- rep(NA, 22)
## for (cx in 1:22) {
## tmp <- quantile(plotpos[which(chr == cx | chr == paste("chr", cx, sep = ""))], probs = c(0, 0.5, 1), na.rm = TRUE)
## minpos[cx] <- tmp[1]
## medpt[cx] <- tmp[2]
## maxpos[cx] <- tmp[3]
## }
## return (list(minpos = minpos, midpt = (minpos+maxpos)/2, medpt = medpt, maxpos = maxpos))
## }
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