Nothing
chrPlot2 <- function(chrData, chrSeg, deb = 100, fin = 1e10) {
positions <- chrData$Position
ndata <- length(positions)
mega <- 1e6
lBounds <- chrSeg[,3]
uBounds <- chrSeg[,4]
if ((deb < 0) || (fin < 0) || (fin < deb)) {
chr <- unique(chrData$Chromosome)
xax <- positions/mega
yax <- chrData$f.L2R
ymin <- min(yax); ymin <- min(ymin, -1.1)
ymax <- max(yax); ymax <- max(ymax, 1.1)
iseg_s <- chrSeg[,1]
iseg_e <- chrSeg[,2]
segVal <- chrSeg[,5]
nseg <- length(iseg_s)
} else {
if (deb < positions[1]) { deb <- positions[1] }
if (fin > positions[ndata]) { fin <- positions[ndata] }
i <- 1; t1 <- i;
while (deb > positions[i]) { t1 <- i; i <- i+1 }
t2 <- i
while (positions[i] < fin) { t2 <- i; i <- i+1 }
chr <- unique(chrData$Chromosome[t1:t2])
xax <- positions[t1:t2]/mega
yax <- chrData$f.L2R[t1:t2]
ymin <- min(yax); ymin <- min(ymin, -1.1)
ymax <- max(yax); ymax <- max(ymax, 1.1)
iseg_s <- chrSeg[,1]
iseg_e <- chrSeg[,2]
segVal <- chrSeg[,5]
nseg <- length(iseg_s)
if ((iseg_e[nseg] < t1) || (iseg_s[1] > t2)) {
t3 <- 0
} else if ((iseg_s[1] > t1) && (iseg_e[nseg] < t2)) {
t3 <- 1; t4 <- nseg
} else if ((iseg_s[1] < t1) && (iseg_e[nseg]<t2)) {
i <- 1; t3 <- i
while (iseg_s[i] < t1) { t3 <- i+1; i <- i+1}
t4 <- nseg
} else if ((iseg_s[1] > t1) && (iseg_e[nseg] > t2)) {
t3 <- 1
i <- nseg; t4 <- i
while (iseg_s[i] > t2) { t4 <- i-1; i <- i-1}
} else {
i <- 1; t3 <- i
while (iseg_s[i] < t1) { t3 <- i+1; i <- i+1}
i <- nseg; t4 <- i
while (iseg_s[i] > t2) { t4 <- i-1; i <- i-1}
}
if (t3) {
iseg_s <- iseg_s[t3:t4]
iseg_e <- iseg_e[t3:t4]
segVal <- segVal[t3:t4]
nseg <- length(iseg_s)
} else {
nseg <- 0
}
}
plot(xax, yax, ylim = c(ymin, ymax), cex = .8, xlab = "x 10^6", ylab = "Log2 Ratio", main = chr)
abline(h = 0, col = "black")
if (nseg) {
for (i in 1:nseg) {
fax <- segVal[i]
np <- iseg_e[i]-iseg_s[i]+1
xax <- positions[iseg_s[i]:iseg_e[i]]/mega
if (fax <0) {
yax <- c(rep(-1, np))
lines(xax, yax, col = "blue", type = "b", cex = 0.6, pch = 24)
} else {
yax <- c(rep(1, np))
lines(xax, yax, col = "red", type = "b", cex = 0.6, pch = 25)
}
}
} else {
}
}
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