From 33db38c966f145b2f47bd7b34abfa9700c04364a Mon Sep 17 00:00:00 2001
From: lizji1992 <lizji1992@gmail.com>
Date: Thu, 19 Sep 2019 14:36:57 -0700
Subject: [PATCH] plot end sequences in boxes

---
 rscripts/simulate_continuous.R | 41 ++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100755 rscripts/simulate_continuous.R

diff --git a/rscripts/simulate_continuous.R b/rscripts/simulate_continuous.R
new file mode 100755
index 0000000..6f0a7e6
--- /dev/null
+++ b/rscripts/simulate_continuous.R
@@ -0,0 +1,41 @@
+args = commandArgs(trailingOnly=TRUE)
+dat <- read.table(args[1])
+dat <- dat[,order(-1:-ncol(dat))]
+#dat <- log(dat[,order(-1:-ncol(dat))]+1)
+
+n.sample <- 100
+time <- 1
+
+pdf(file=args[2],
+    width=7, height=3, pointsize=8)
+
+layout(matrix(c(1,2,3), 3, 1, byrow = TRUE), 
+       heights=c(1, 5, 1))
+
+root <- dat[, ncol(dat)]
+leaf <- dat[, 1]
+
+# root
+par(mar=c(0.5, 4, 3.5, 4))
+print(dim(dat))
+image(as.matrix(root), col=gray((n.sample:0)/n.sample),
+      useRaster=TRUE, axes=FALSE, xlab="", ylab="")
+box()
+
+# paths
+par(mar=c(0, 4, 0, 4))
+image(as.matrix(dat), col=gray((n.sample:0)/n.sample),
+      useRaster=TRUE, axes=FALSE, xlab="", ylab="Time")
+axis(2, at = seq(0, 1, by = 1/10),
+     labels = seq(0, time, by = time/10))
+box()
+
+# leaf
+par(mar=c(3.5, 4, 0.5, 4))
+image(as.matrix(leaf), col=gray((n.sample:0)/n.sample),
+      useRaster=TRUE, axes=FALSE, xlab="Sites", ylab="", mgp=c(2.5, 0.1, 0))
+axis(1, at = seq(0, 1, by = 1/10),
+     labels = seq(0, nrow(dat), by = nrow(dat)/10))
+box()
+
+dev.off()