png("scanone.png", width = 960, height = 720)
plot(out.em, chr = c(1,4,6,15), lwd = 4)
plot(out.hk, chr = c(1,4,6,15), add = TRUE, lty = 2, lwd = 4)
dev.off()

png("permone.png", width = 960, height = 720)
plot(out.em, chr = c(1,4,6,15), lwd = 4)
plot(out.hk, chr = c(1,4,6,15), add = TRUE, lty = 2, lwd = 4)
tmp <- summary(operm.hk, alpha=c(0.01,0.05))
abline(h = tmp, lty = 3, lwd = 4)
text(rep(0,2), tmp + 0.35, row.names(tmp), cex = 2, adj = 0)
dev.off()

png("scantwo.png", width = 960, height = 720)
plot(out2.hk, chr=c(1,4,6,15), col = "gray")
dev.off()

png("compone.png", width = 960, height = 600)
par(mfrow = c(2,1), mar = c(4,4,3,0))
plot(one, scan = "main", chr = c(1,4,6,15), lwd = 4)
plot(out.em, chr=c(1,4,6,15), lty = 4, lwd = 4, add = TRUE)
plot(one, scan = "epistasis", chr = c(1,4,6,15), lwd = 4)
dev.off()

png("best.png", width = 960, height = 720)
plot(best, col = "black")
dev.off()

png("close.png", width = 960, height = 600)
trellis.par.set(box.umbrella = list(col = "black"),
  box.rectangle = list(col = "black"), plot.symbol = list(col = "black"))
plot(close, more = TRUE, split = c(1,1,2,1))
plot(close, category = "nqtl", split = c(2,1,2,1))
dev.off()

png("hpd.png", width = 960, height = 600)
plot(hpd,
  col = c(sum="black", epistasis = "black", main = "black",
          H = "black", A = "black"),
  lty = c(3,2,1), lwd = 4)
dev.off()

png("slicetwo.png", width = 960, height = 720)
plot(slice, figs = c("effects", "cellmean", "effectplot"),
  lwd = 4, col = c(AA="black",HA="black",AH="darkgray",HH="darkgray"),
  lty = 1:4)
dev.off()