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bsaplot.r
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bsaplot.r
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bsaplot <- function(
key,
chrom,
chrmax,
chrmin = 1,
linef = NULL,
linep = c(1, 2),
linev = c(3, 4),
linec = c("black", "blue", "red", "blue", "red"),
pointf = NULL,
pointp = c(1, 2),
pointv = 3,
pointc = c("#33A02C", "#FF7F00"),
hline = NULL,
hcolor = "grey",
hlty = 1,
ymin = -1,
ymax = 1,
xlab = "Chromosome",
ylab = expression(Delta(SNPindex)),
cexa = 1.5,
cexl = 2,
cexp = 0.4,
pch = 19,
lwd = 3,
las = 1,
bandc = "grey90",
alt = F,
width = 15,
height = 6,
res = 600
){
library(gtools)
multi.mixedorder <- function(..., na.last = TRUE, decreasing = FALSE){
do.call(order, c(
lapply(list(...), function(l){
if(is.character(l)){
factor(l, levels=mixedsort(unique(l)))
} else {
l
}
}),
list(na.last = na.last, decreasing = decreasing)
))
}
## global deal
chrom <- as.character(chrom)
mindf <- data.frame(chr = chrom, pos = chrmin, stringsAsFactors = F)
maxdf <- data.frame(chr = chrom, pos = chrmax, stringsAsFactors = F)
minmax <- rbind(mindf, maxdf)
minmax <- minmax[multi.mixedorder(minmax[,1], minmax[,2]), ]
chrom <- mixedsort(chrom)
mins <- NULL
maxs <- NULL
print("pass1: global")
## line deal
if(!is.null(linef)){
linet <- read.table(linef, header = T, stringsAsFactors = F, check.names = F)
linet <- linet[,c(linep, linev)]
linet[, 1] <- as.character(linet[, 1])
linet <- linet[linet[, 1] %in% chrom, ]
lminmax <- minmax
for(i in 3:ncol(linet)){
lminmax[,i] <- NA
}
names(lminmax) <- names(linet)
linet <- rbind(linet, lminmax)
linet <- linet[multi.mixedorder(linet[,1], linet[,2]),]
mins <- min(linet[, 3:ncol(linet)], na.rm = T)
maxs <- max(linet[, 3:ncol(linet)], na.rm = T)
class(linet) <- c("scanone", "data.frame")
}
print("pass2: line data")
## point deal
if(!is.null(pointf)){
pointc <- rep(pointc, ceiling(length(chrom)/length(pointc)))[1:length(chrom)]
chrcolor <- data.frame(chrom, pointc, stringsAsFactors = F)
pointt <- read.table(pointf, header = T, stringsAsFactors = F, check.names = F)
pointt <- pointt[,c(pointp, pointv)]
pointt[, 1] <- as.character(pointt[, 1])
pointt <- pointt[pointt[, 1] %in% chrom,]
pminmax <- minmax
for(i in 3:ncol(pointt)){
pminmax[,i] <- NA
}
names(pminmax) <- names(pointt)
names(pminmax) <- names(pointt)
pointt <- rbind(pointt, pminmax)
pointt <- pointt[multi.mixedorder(pointt[,1], pointt[,2]),]
if(is.null(mins)){
mins <- min(pointt[,3], na.rm = T)
}else{
mins <- min(min(pointt[,3], na.rm = T), mins)
}
if(is.null(maxs)){
maxs <- max(pointt[,3], na.rm = T)
}else{
maxs <- max(max(pointt[,3], na.rm = T), maxs)
}
class(pointt) <- c("scanone", "data.frame")
}
print("pass3: point data")
## plot
if(is.null(ymin)){
ymin <- mins
}
if(is.null(ymax)){
ymax <- maxs
}
minmax$lod <- NA
class(minmax) <- c("scanone", "data.frame")
# png
png(filename = paste0(key, ".plplot.png"), width = width, height = height, units = "in", res = res)
dev.control("enable")
# global parameters
chara_len <- max(nchar(chrom))
marx <- 5
if(chara_len > 6){
marx <- marx * chara_len/5
}
par(mgp = c(2.5, 0.8, 0), mai = c(0.8, 1, 0.2, 0.2),
mar = c(marx,5,0.8,0.8), cex.axis = cexa, cex.lab = cexl)
# empty plot
plot.scanone(x = minmax, type="n", ylim = c(ymin, ymax), bty = "n",
bandcol = bandc, incl.markers = F, yaxs="i", alternate.chrid = alt,
xlab = xlab, ylab = ylab, las = las)
box()
# point plot
if(!is.null(pointf)){
nchr <- length(chrcolor[,2])
if(nchr > 1){
for (i in 1:nchr) {
ptmp <- pointt
ptmp[ptmp[, 1] != chrcolor[i, 1], ][, 3] <- NA
plot.scanone(ptmp, add = T, lodcolumn = 1, col = chrcolor[i, 2], type = "p", pch = pch, cex = cexp)
}
}else{
ptmp <- pointt
plot.scanone(ptmp, add = T, lodcolumn = 1, col = chrcolor[,2], type = "p", pch = pch, cex = cexp)
}
print("pass4: point plot")
}
# hline
if(!is.null(hline)){
abline(h = hline, lty = hlty, col = hcolor, lwd = lwd)
}
# line plot
if(!is.null(linef)){
for (l in 1:(ncol(linet) - 2)) {
plot.scanone(linet, add=T, lodcolumn = l, col = linec[l], type = "l",
pch = pch, lwd = lwd, cex = cexp)
}
print("pass5: line plot")
}
# box
#box()
# copy to pdf
dev.copy(pdf, file = paste0(key, ".plplot.pdf"), width = width, height = height)
dev.off(which = dev.cur())
# close all image device
for (i in 1:length(dev.list())) {
dev.off()
}
}