--- a/signature.r	Tue Jan 07 06:59:56 2020 -0500
+++ b/signature.r	Sat Oct 23 22:55:19 2021 +0000
@@ -1,6 +1,10 @@
 ## Setup R error handling to go to stderr
-#options(show.error.messages=F,
-        #error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F,
+        error = function() {
+            cat(geterrmessage(), file = stderr())
+            q("no", 1, F)
+        }
+)
 warnings()
 
 library(RColorBrewer)
@@ -11,89 +15,90 @@
 library(optparse)
 
 option_list <- list(
-    make_option("--h_dataframe", type="character", help="path to h-signature dataframe"),
-    make_option("--z_dataframe", type="character", help="path to z-signature dataframe"),
-    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("--h_dataframe", type = "character",
+                help = "path to h-signature dataframe"),
+    make_option("--z_dataframe", type = "character",
+                help = "path to z-signature dataframe"),
+    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")
     )
- 
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
-args = parse_args(parser)
-
-
-
+args <- parse_args(parser)
  
 # data frames implementation
-h_dataframe = read.delim(args$h_dataframe, header=F)
-colnames(h_dataframe) = c("chrom", "overlap", "sig", "z-score")
-h_dataframe$sig = h_dataframe$sig * 100  # to get probs in %
-z_dataframe = read.delim(args$z_dataframe, header=F)
-colnames(z_dataframe) = c("chrom", "overlap", "sig", "z-score")
+h_dataframe <- read.delim(args$h_dataframe, header = F)
+colnames(h_dataframe) <- c("chrom", "overlap", "sig", "z-score")
+h_dataframe$sig <- h_dataframe$sig * 100  # to get probs in %
+z_dataframe <- read.delim(args$z_dataframe, header = F)
+colnames(z_dataframe) <- c("chrom", "overlap", "sig", "z-score")
 
 # functions
-      globalgraph = function () {
+    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)
+        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, 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(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 [%]", ylim = c(0, 50), pch = 19,
+             col = "darkslateblue", lwd = 2)
 
-        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2,4)],
-             type = "l", main="Overlap Probability Z-scores", cex.main=1,
-             xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2,
-             col="darkslateblue", lwd=2)
-
-        mtext(args$title, outer = TRUE, cex=1)
+        plot(h_dataframe[h_dataframe$chrom == "all_chromosomes", c(2, 4)],
+             type = "l", main = "Overlap Probability Z-scores", cex.main = 1,
+             xlab = "overlap (nt)", ylab = "z-score", pch = 19, cex = 0.2,
+             col = "darkslateblue", lwd = 2)
+        mtext(args$title, outer = TRUE, cex = 1)
         dev.off()
-      }
+    }
 
-      treillisgraph = function (df, ...) {
-          pdf(args$pdf, paper="special", height=11.69, width=6 ) # 8.2677
-          p = xyplot(sig ~ overlap|factor(method, levels=unique(method))+chrom, data = df,
+    treillisgraph <- function(df, ...) {
+          pdf(args$pdf, paper = "special", height = 11.69, width = 6)
+          p <- xyplot(sig ~ overlap | factor(method, levels = unique(method)) + chrom,
+                   data = df,
                    type = "l",
-                   col='darkblue',
-                   cex=0.5,
-                   scales=list(y=list(tick.number=4, relation="free", cex=0.6, rot=0), x=list(cex=0.6, alternating=FALSE)),
+                   col = "darkblue",
+                   cex = 0.5,
+                   scales = list(y = list(tick.number = 4, relation = "free", cex = 0.6,
+                                          rot = 0),
+                                 x = list(cex = 0.6, alternating = FALSE)),
                    xlab = "Overlap",
                    ylab = "signature (Nbr of pairs / Overlap prob.)",
                    main = args$title,
-                   par.strip.text=list(cex=.5),
-                   pch=19, lwd =2,
-                   as.table=TRUE,
-                   layout=c(2,12),
+                   par.strip.text = list(cex = .5),
+                   pch = 19, lwd = 2,
+                   as.table = TRUE,
+                   layout = c(2, 12),
                    newpage = T,
                    ...)
-           plot(p) 
+           plot(p)
            dev.off()
-      }
+    }
 
 # main
 
-if (args$plot_method=="global") {
+if (args$plot_method == "global") {
     globalgraph()
-    }
+}
 
-if(args$plot_method=="lattice") {
+if (args$plot_method == "lattice") {
     # rearrange dataframes
-    h_sig = h_dataframe[,c(1,2,3)]
-    h_sig = cbind(rep("Overlap Prob (%)", length(h_sig[,1])), h_sig)
-    colnames(h_sig) = c("method", "chrom", "overlap", "sig")
-    z_pairs = z_dataframe[,c(1,2,3)]
-    z_pairs = cbind(rep("Nbr of pairs", length(z_pairs[,1])), z_pairs)
-    colnames(z_pairs) = c("method", "chrom", "overlap", "sig")
-    lattice_df = rbind(z_pairs, h_sig)
-    par.settings.treillis=list(strip.background = list(
+    h_sig <- h_dataframe[, c(1, 2, 3)]
+    h_sig <- cbind(rep("Overlap Prob (%)", length(h_sig[, 1])), h_sig)
+    colnames(h_sig) <- c("method", "chrom", "overlap", "sig")
+    z_pairs <- z_dataframe[, c(1, 2, 3)]
+    z_pairs <- cbind(rep("Nbr of pairs", length(z_pairs[, 1])), z_pairs)
+    colnames(z_pairs) <- c("method", "chrom", "overlap", "sig")
+    lattice_df <- rbind(z_pairs, h_sig)
+    par_settings_treillis <- list(strip.background = list(
             col = c("lightblue", "lightgreen")))
-
-    treillisgraph(lattice_df, par.settings=par.settings.treillis)    
+    treillisgraph(lattice_df, par.settings = par_settings_treillis)
 }