--- a/signature.r	Sat Feb 25 09:54:28 2023 +0000
+++ b/signature.r	Thu Apr 06 23:00:54 2023 +0000
@@ -22,7 +22,12 @@
     make_option("--plot_method", type = "character",
                 help = "How  data should be plotted (global or lattice)"),
     make_option("--pdf", type = "character", help = "path to the pdf file with plots"),
-    make_option("--title", type = "character", help = "Graph Title")
+    make_option("--title", type = "character", help = "Graph Title"),
+
+    make_option("--npairs_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Numbers-of-pairs plot"),
+    make_option("--npairszscore_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Number-of-pairs-Z−scores plot"),
+    make_option("--overlapprob_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Overlap-probabilities plot"),
+    make_option("--overlapprobzscore_ylim", type = "integer", default = 0, help = "Maximum of Y-scale of the Overlap-probabilities-Z−scores plot")
     )
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
 args <- parse_args(parser)
@@ -34,28 +39,64 @@
 z_dataframe <- read.delim(args$z_dataframe, header = FALSE)
 colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
 
+# graph limits parameters
+if (args$npairs_ylim == 0) {
+    npairs_ylim <- NULL
+    } else {
+    npairs_ylim <- c(0, args$npairs_ylim)
+}
+
+if (args$npairszscore_ylim == 0) {
+    npairszscore_ylim <- NULL
+    } else {
+    npairszscore_ylim <- c(0, args$npairszscore_ylim)
+}
+
+if (args$overlapprob_ylim == 0) {
+    overlapprob_ylim <- NULL
+    } else {
+    overlapprob_ylim <- c(0, args$overlapprob_ylim)
+}
+
+if (args$overlapprobzscore_ylim == 0) {
+    overlapprobzscore_ylim <- NULL
+    } else {
+    overlapprobzscore_ylim <- c(0, args$overlapprobzscore_ylim)
+}
+
+
 # functions
     globalgraph <- function() {
         pdf(args$pdf)
         par(mfrow = c(2, 2), oma = c(0, 0, 3, 0))
-        plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)],
-             type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)",
-             ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4)
 
-        plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)],
-             type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)",
-             ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2)
+            plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 3)],
+                     type = "h", main = "Numbers of pairs", cex.main = 1, xlab = "overlap (nt)",
+                     ylab = "Numbers of pairs", col = "darkslateblue", lwd = 4,
+                     ylim = npairs_ylim
+                     )
+
+            plot(z_dataframe[z_dataframe$chrom == "all_chromosomes", c(2, 4)],
+                     type = "l", main = "Number of pairs Z-scores", cex.main = 1, xlab = "overlap (nt)",
+                     ylab = "z-score", pch = 19, cex = 0.2, col = "darkslateblue", lwd = 2,
+                     ylim = npairszscore_ylim
+                     )
 
-        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)],
-             type = "l", main = "Overlap probabilities", cex.main = 1,
-             xlab = "overlap (nt)",
-             ylab = "Probability [%]", ylim = c(0, 50), pch = 19,
-             col = "darkslateblue", lwd = 2)
+            plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 3)],
+                     type = "l", main = "Overlap probabilities", cex.main = 1,
+                     xlab = "overlap (nt)",
+                     ylab = "Probability [%]", pch = 19,
+                     col = "darkslateblue", lwd = 2,
+                     ylim = overlapprob_ylim
+                     )
 
-        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
-             type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
-             xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
-             col = "darkslateblue", lwd = 2)
+            plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
+                     type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
+                     xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
+                     col = "darkslateblue", lwd = 2,
+                     ylim = overlapprobzscore_ylim
+                     )
+
         mtext(args$title, outer = TRUE, cex = 1)
         dev.off()
     }