--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chromeister/bin/plot_diags.R	Wed Dec 12 07:18:40 2018 -0500
@@ -0,0 +1,179 @@
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+if(length(args) < 1){
+  stop("USE: Rscript --vanilla plot.R <matrix>")
+}
+
+
+path_mat = args[1]
+
+
+
+
+data <- as.matrix(read.csv(path_mat, sep = " "))
+percentage <- 0.1
+
+
+
+
+d <- col(data) - row(data)
+groups <- split(data, d)
+acum <- c()
+for(i in 1:length(groups)){
+  acum <- c(acum, sum(unlist(groups[i])))
+}
+
+
+# reverse
+data_r <- data
+for(i in 1:length(data_r[,1])){
+  data_r[i,] <- rev(data_r[i,])
+}
+d <- col(data_r) - row(data_r)
+groups <- split(data_r, d)
+acum_r <- c()
+for(i in 1:length(groups)){
+  acum_r <- c(acum, sum(unlist(groups[i]))/length(unlist(groups[i])) )
+}
+
+indexes <- matrix(0, nrow=length(acum), ncol = 3)
+indexes[,1] <- c(1:length(acum))
+indexes[,2] <- acum
+
+#sort
+indexes[order(indexes[,2], decreasing=TRUE),]
+
+#crop by percentage
+n_percent <- percentage * length(acum)
+
+for(i in 1:n_percent){
+  indexes[i,3] <- 1
+}
+
+# Now resort based on first column to have them again in order
+indexes[order(indexes[,1], decreasing=FALSE),]
+
+
+# same in reverse
+#put into indexes to sort
+indexes_r <- matrix(0, nrow=length(acum_r), ncol = 3)
+indexes_r[,1] <- c(1:length(acum_r))
+indexes_r[,2] <- acum_r
+
+#sort
+indexes_r[order(indexes_r[,2], decreasing=TRUE),]
+
+#crop by percentage
+n_percent <- percentage * length(acum_r)
+
+for(i in 1:n_percent){
+  indexes_r[i,3] <- 1
+}
+
+# Now resort based on first column to have them again in order
+indexes_r[order(indexes_r[,1], decreasing=FALSE),]
+
+
+
+
+finalmat <- matrix(0, nrow=length(data[,1]), ncol=length(data[1,]))
+
+
+for(i in length(data[1,]):1){
+  x <- i
+  y <- 1
+
+  if(indexes[i,3] == 1){
+    while(x < length(data[1,]) && y <= length(data[,1])){
+      
+      
+      if(x < length(data[1,]) && y <= length(data[,1])){
+        finalmat[x,y] <- 1  
+      }
+      
+      y <- y + 1
+      x <- x + 1
+      
+      
+    }  
+  }
+  
+}
+
+for(i in 2:length(data[,1])){
+  x <- 1
+  y <- i
+  
+  if(indexes[i,3] == 1){
+    
+    while(x < length(data[1,]) && y <= length(data[,1])){
+      
+      if(x < length(data[1,]) && y <= length(data[,1])){
+        finalmat[x,y] <- 1
+      }
+      y <- y + 1
+      x <- x + 1
+      
+    }  
+  }
+}
+
+
+#same for reverse
+for(i in length(data_r[1,]):1){
+  x <- i
+  y <- 1
+  
+  if(indexes[i,3] == 1){
+    while(x < length(data_r[1,]) && y <= length(data_r[,1])){
+      
+      
+      if(x < length(data_r[1,]) && y <= length(data_r[,1])){
+        finalmat[x,length(data_r[,1])-y] <- 1  
+      }
+      
+      y <- y + 1
+      x <- x + 1
+      
+      
+    }  
+  }
+  
+}
+
+for(i in 2:length(data_r[,1])){
+  x <- 1
+  y <- i
+  
+  if(indexes[i,3] == 1){
+    
+    while(x < length(data_r[1,]) && y <= length(data_r[,1])){
+      
+      if(x < length(data_r[1,]) && y <= length(data_r[,1])){
+        finalmat[x,length(data_r[,1])-y] <- 1
+      }
+      y <- y + 1
+      x <- x + 1
+      
+    }  
+  }
+}
+
+# fully write last
+
+for(i in 1:length(data[,1])){
+  for(j in 1:length(data[1,])){
+    if(finalmat[i,j] == 0){
+      
+      data[i,j] <- 0
+    }
+  }
+}
+
+png(paste(path_mat, ".png", sep=""), width = length(data[,1]), height = length(data[,1]))
+image((data), col = grey(seq(1, 0, length = 256)), xaxt='n', yaxt='n')
+dev.off()
+
+
+