changeset 8:eb2aa7cffca3 draft default tip

Uploaded

--- a/RScript.r	Tue Dec 12 04:53:20 2017 -0500
+++ b/RScript.r	Wed Dec 13 06:00:44 2017 -0500
@@ -420,7 +420,9 @@
     } else {
       p = ggplot(NULL, aes(x=c("In one", "In Both"),y=0)) + geom_blank(NULL) + xlab("In one or both of the samples") + ylab(onShort) + ggtitle(paste(patient1[1,"Patient"], patient1[1,"Sample"], patient2[1,"Sample"], onShort, product[iter, "Titles"]))
     }
-    png(paste(patient1[1,"Patient"], "_", patient1[1,"Sample"], "_", patient2[1,"Sample"], "_", onShort, "_", product[iter, "Titles"],"_scatter.png", sep=""))
+	file_name = paste(patient1[1,"Patient"], "_", patient1[1,"Sample"], "_", patient2[1,"Sample"], "_", onShort, "_", product[iter, "Titles"],"_scatter.png", sep="")
+	print(paste("Writing figure:", file_name))
+    png(file_name)
     print(p)
     dev.off()
     if(sum(both) > 0){
@@ -450,7 +452,9 @@
   plt = plt + geom_text(aes(ymax=max(Both), x=cut_off_value,y=Both,label=Both), angle=90, hjust=0)
   plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in both")
   plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
-  png(paste(patient, "_", onShort, ".png", sep=""), width=1920, height=1080)
+  file_name = paste(patient, "_", onShort, ".png", sep="")
+  print(paste("Writing figure:", file_name))
+  png(file_name, width=1920, height=1080)
   print(plt)
   dev.off()
   #(t,r,b,l)
@@ -460,7 +464,10 @@
   plt = plt + geom_text(aes(ymax=max(percentage), x=cut_off_value,y=percentage,label=percentage), angle=90, hjust=0)
   plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("% clones in both left and right")
   plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
-  png(paste(patient, "_percent_", onShort, ".png", sep=""), width=1920, height=1080)
+  
+  file_name = paste(patient, "_percent_", onShort, ".png", sep="")
+  print(paste("Writing figure:", file_name))
+  png(file_name, width=1920, height=1080)
   print(plt)
   dev.off()
   
@@ -474,7 +481,9 @@
   plt = plt + geom_text(data=patientResult[patientResult$variable == oneSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=-0.2)
   plt = plt + geom_text(data=patientResult[patientResult$variable == twoSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=0.8)
   plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle(paste("Number of clones in only ", oneSample, " and only ", twoSample, sep=""))
-  png(paste(patient, "_", onShort, "_both.png", sep=""), width=1920, height=1080)
+  file_name = paste(patient, "_", onShort, "_both.png", sep="")
+  print(paste("Writing figure:", file_name))
+  png(file_name, width=1920, height=1080)
   print(plt)
   dev.off()
 }
@@ -506,7 +515,9 @@
 	p = p + geom_point(aes(colour=type), position="jitter")
 	p = p + xlab("In one or both samples") + ylab("Reads")
 	p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the reads of the patients with a single sample")
-	png("singles_reads_scatterplot.png", width=640 * length(unique(single_patients$Patient)) + 100, height=1080)
+	file_name = "singles_reads_scatterplot.png"
+  	print(paste("Writing figure:", file_name))
+	png(file_name, width=640 * length(unique(single_patients$Patient)) + 100, height=1080)
 	print(p)
 	dev.off()
 
@@ -515,7 +526,9 @@
 	p = p + geom_point(aes(colour=type), position="jitter")
 	p = p + xlab("In one or both samples") + ylab("Frequency")
 	p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the frequency of the patients with a single sample")
-	png("singles_freq_scatterplot.png", width=640 * length(unique(single_patients$Patient)) + 100, height=1080)
+	file_name = "singles_freq_scatterplot.png"
+  	print(paste("Writing figure:", file_name))
+	png(file_name, width=640 * length(unique(single_patients$Patient)) + 100, height=1080)
 	print(p)
 	dev.off()
 } else {
@@ -948,7 +961,9 @@
 		} else {
 			p = ggplot(NULL, aes(x=c("In one", "In multiple"),y=0)) + geom_blank(NULL) + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
 		}
-		png(paste(label1, "_", label2, "_", label3, "_", onShort, "_", product[iter, titleIndex],"_scatter.png", sep=""))
+		file_name = paste(label1, "_", label2, "_", label3, "_", onShort, "_", product[iter, titleIndex],"_scatter.png", sep="")
+  		print(paste("Writing figure:", file_name))
+		png(file_name)
 		print(p)
 	  dev.off()
 	} 
@@ -982,7 +997,9 @@
 	plt = plt + geom_text(aes(ymax=max(All), x=cut_off_value,y=All,label=All), angle=90, hjust=0)
 	plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in All")
 	plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
-	png(paste(label1, "_", label2, "_", label3, "_", onShort, "_total_all.png", sep=""), width=1920, height=1080)
+	file_name = paste(label1, "_", label2, "_", label3, "_", onShort, "_total_all.png", sep="")
+	print(paste("Writing figure:", file_name))
+	png(file_name, width=1920, height=1080)
 	print(plt)
 	dev.off()
 
@@ -1000,7 +1017,9 @@
 	plt = plt + geom_text(data=patientResult[patientResult$variable == twoSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=0.4, size=fontSize)
 	plt = plt + geom_text(data=patientResult[patientResult$variable == threeSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=1.5, size=fontSize)
 	plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in only one sample")
-	png(paste(label1, "_", label2, "_", label3, "_", onShort, "_indiv_all.png", sep=""), width=1920, height=1080)
+	file_name = paste(label1, "_", label2, "_", label3, "_", onShort, "_indiv_all.png", sep="")
+	print(paste("Writing figure:", file_name))
+	png(file_name, width=1920, height=1080)
 	print(plt)
 	dev.off()
 }