library(qtlbim)
data(Bnapus)
Bnapus <- calc.genoprob(Bnapus, step = 2, error = 0.01)
###########################################
fl8 <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower8"))
fl4 <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower4"))
fl8.4a <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower8"),
  addcov = Bnapus$pheno$log10flower4)
fl8.4 <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower8"),
  intcov = Bnapus$pheno$log10flower4)
plot(fl4, fl8, fl8.4, chr = "N2", col = rep(1,3), lty = 1:3)
###########################################
png("Bnapuspair.png", width = 960, height = 720)
par(mfrow = c(1,2), mar = c(4.1,4.1,3.1,0.1))
plot(Bnapus$pheno$log10flower4,Bnapus$pheno$log10flower8,
  cex = 4, lwd = 2,
  xlab = "log10(4 week flower)", ylab = "log10(8 week flower)")
fit <- lm(log10flower8 ~ log10flower4, Bnapus$pheno)
tmp <- range(Bnapus$pheno$log10flower4, na.rm = TRUE) 
lines(tmp, predict(fit, data.frame(log10flower4 = tmp)),
  lwd = 4, col = "darkgray")
plot(fl4, fl8, chr = "N2", col = rep(1,2), lty = 1:2,
  main = "solid = 4wk, dashed = 8wk", lwd = 4)
dev.off()

png("Bnapusscan.png", width = 960, height = 720)
plot(fl8, fl8.4a, fl8.4, chr = "N2", col = rep(1,3), lty = 1:3,
  main = "solid = 8wk, dashed = addcov, dotted = intcov")
dev.off()

library(lattice)
markers <- c("E38M50.133","ec2e5a","wg7f3a")
tmpdata <- data.frame(pull.geno(Bnapus)[,markers])
tmpdata$fl4 <- Bnapus$pheno$log10flower4
tmpdata$fl8 <- Bnapus$pheno$log10flower8
png("Bnapuscov.png", width = 960, height = 720)
print(xyplot(fl8 ~ fl4, tmpdata, group = wg7f3a,
  col = "black", pch = 3:4, cex = 2, type = c("p","r"),
  xlab = "log10(4wk flower time)",
  ylab = "log10(8wk flower time)",
  main = "marker at 47cM"),
  more = TRUE, split = c(1,1,2,1))
print(xyplot(fl8 ~ fl4, tmpdata, group = E38M50.133,
  col = "black", pch = 3:4, cex = 2, type = c("p","r"),
  xlab = "log10(4wk flower time)",
  ylab = "log10(8wk flower time)",
  main = "marker at 80cM"),
  split = c(2,1,2,1))
dev.off()

fl4 <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower4"))
fl4.8 <- scanone(Bnapus,, find.pheno(Bnapus, "log10flower4"),
  intcov = Bnapus$pheno$log10flower8)
plot(fl4, fl4.8, chr = "N2")

Fl4 <- scantwo(Bnapus, "N2", find.pheno(Bnapus, "log10flower4"))
Fl8 <- scantwo(Bnapus, "N2", find.pheno(Bnapus, "log10flower8"))
Fl8.4 <- scantwo(Bnapus, "N2", find.pheno(Bnapus, "log10flower8"),
  intcov = Bnapus$pheno$log10flower4)
Fl4.8 <- scantwo(Bnapus, "N2", find.pheno(Bnapus, "log10flower4"),
  intcov = Bnapus$pheno$log10flower8)
plot(Fl4)
x11()
plot(Fl4.8)
plot(Fl8)
x11()
plot(Fl8.4)