Mercurial > repos > davidvanzessen > shm_csr

changeset 42:1cf60ae234b4 draft

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Uploaded
author davidvanzessen
date Tue, 28 Mar 2017 08:25:36 -0400
parents b8ac74723ab0
children 77a7ac76c7b9
files aa_histogram.r pattern_plots.r shm_csr.r wrapper.sh
diffstat 4 files changed, 42 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/aa_histogram.r	Tue Mar 14 09:30:16 2017 -0400
+++ b/aa_histogram.r	Tue Mar 28 08:25:36 2017 -0400
@@ -64,4 +64,6 @@
 	png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
 	print(m)
 	dev.off()
+	
+	ggsave(paste(outdir, "/aa_histogram_", gene, ".pdf", sep=""), m, width=14, height=7)
 }
--- a/pattern_plots.r	Tue Mar 14 09:30:16 2017 -0400
+++ b/pattern_plots.r	Tue Mar 28 08:25:36 2017 -0400
@@ -9,21 +9,22 @@
 plot1.path = args[2]
 plot1.png = paste(plot1.path, ".png", sep="")
 plot1.txt = paste(plot1.path, ".txt", sep="")
+plot1.pdf = paste(plot1.path, ".pdf", sep="")
 
 plot2.path = args[3]
 plot2.png = paste(plot2.path, ".png", sep="")
 plot2.txt = paste(plot2.path, ".txt", sep="")
+plot2.pdf = paste(plot2.path, ".pdf", sep="")
 
 plot3.path = args[4]
 plot3.png = paste(plot3.path, ".png", sep="")
 plot3.txt = paste(plot3.path, ".txt", sep="")
+plot3.pdf = paste(plot3.path, ".pdf", sep="")
 
 clean.output = args[5]
 
 dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T, row.names=1)
 
-
-
 classes = c("IGA", "IGA1", "IGA2", "IGG", "IGG1", "IGG2", "IGG3", "IGG4", "IGM", "IGE")
 xyz = c("x", "y", "z")
 new.names = c(paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))
@@ -63,6 +64,8 @@
 print(p)
 dev.off()
 
+ggsave(plot1.pdf, p)
+
 data2 = dat[c(1, 5:8),]
 
 data2 = data2[,names(data2)[grepl("\\.x", names(data2))]]
@@ -100,6 +103,8 @@
 print(p)
 dev.off()
 
+ggsave(plot2.pdf, p)
+
 data3 = dat[c(5, 6, 8, 17:20),]
 data3 = data3[,names(data3)[grepl("\\.x", names(data3))]]
 names(data3) = gsub(".x", "", names(data3))
@@ -138,6 +143,7 @@
 print(p)
 dev.off()
 
+ggsave(plot3.pdf, p)
 
 
 
@@ -169,3 +175,4 @@
 
 
 
+
--- a/shm_csr.r	Tue Mar 14 09:30:16 2017 -0400
+++ b/shm_csr.r	Tue Mar 28 08:25:36 2017 -0400
@@ -307,11 +307,16 @@
 			#p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black"))
 			print(p)
 			dev.off()
+			
+			ggsave(paste("transitions_stacked_", name, ".pdf", sep=""))
+			
 			png(filename=paste("transitions_heatmap_", name, ".png", sep=""))
 			p = ggplot(transition2, aes(factor(reorder(variable, -order.y)), factor(reorder(id, -order.x)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap
 			p = p + xlab("To base") + ylab("From Base") + ggtitle("Heatmap transition information")  + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"))
 			print(p)
 			dev.off()
+			
+			ggsave(paste("transitions_heatmap_", name, ".pdf", sep=""))
 		} else {
 			#print("No data to plot")
 		}
@@ -394,6 +399,8 @@
 	png(filename="IGA.png")
 	print(pc)
 	dev.off()
+	
+	ggsave("IGA.pdf", pc)
 }
 
 print("Plotting IGG piechart")
@@ -415,6 +422,8 @@
 	png(filename="IGG.png")
 	print(pc)
 	dev.off()
+	
+	ggsave("IGG.pdf", pc)
 }
 
 print("Plotting scatterplot")
@@ -436,6 +445,8 @@
 print(p)
 dev.off()
 
+ggsave("scatter.pdf", p)
+
 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
 print("Plotting frequency ranges plot")
@@ -460,6 +471,8 @@
 print(p)
 dev.off()
 
+ggsave("frequency_ranges.pdf", p)
+
 frequency_bins_data_by_class = frequency_bins_data
 
 frequency_bins_data_by_class = frequency_bins_data_by_class[order(frequency_bins_data_by_class$best_match_class, frequency_bins_data_by_class$frequency_bins),]
--- a/wrapper.sh	Tue Mar 14 09:30:16 2017 -0400
+++ b/wrapper.sh	Tue Mar 28 08:25:36 2017 -0400
@@ -187,6 +187,7 @@
 Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
 if [ -e "$outdir/aa_histogram_.png" ]; then
         mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
+        mv $outdir/aa_histogram_.pdf $outdir/aa_histogram.pdf
         mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
         mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
         mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
@@ -297,9 +298,9 @@
 	#echo "<a href='data_${func}.txt'>Download data</a>" >> $output
 done
 
-echo "<img src='aid_motives.png' /><br />" >> $output
-echo "<img src='relative_mutations.png' /><br />" >> $output
-echo "<img src='abolute_mutations.png' /><br />" >> $output
+echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
+echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
+echo "<a href='abolute_mutations.pdf'><img src='abolute_mutations.png' /></a><br />" >> $output
 echo "<br />" >> $output
 cat $dir/shm_overview.htm >> $output
 echo "</div>" >> $output #SHM overview tab end
@@ -307,15 +308,15 @@
 echo "---------------- images ----------------"
 echo "---------------- images ----------------<br />" >> $log
 
-echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output
+echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'></a>" >> $output
 
 if [ -a $outdir/scatter.png ]
 then
-	echo "<img src='scatter.png'/><br />" >> $output
+	echo "<a href='scatter.pdf'><img src='scatter.png'/><br />" >> $output
 fi
 if [ -a $outdir/frequency_ranges.png ]
 then
-	echo "<img src='frequency_ranges.png'/><br />" >> $output
+	echo "<a href='frequency_ranges.pdf'><img src='frequency_ranges.png'/></a><br />" >> $output
 fi
 
 echo "<br />" >> $output
@@ -334,14 +335,14 @@
 	
 	if [ -e $outdir/transitions_heatmap_${gene}.png ]
 	then
-		echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
+		echo "<td><a href='transitions_heatmap_${gene}.pdf'><img src='transitions_heatmap_${gene}.png' /></a></td>" >> $output
 	else
 		echo "<td></td>" >> $output
 	fi
 	
 	if [ -e $outdir/transitions_stacked_${gene}.png ]
 	then
-		echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
+		echo "<td><a href='transitions_stacked_${gene}.pdf'><img src='transitions_stacked_${gene}.png' /></a></td>" >> $output
 	else
 		echo "<td></td>" >> $output
 	fi
@@ -365,8 +366,8 @@
 
 echo "<tr>" >> $output
 echo "<td><h1>All</h1></td>" >> $output
-echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
-echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
+echo "<td><a href='transitions_heatmap_all.pdf'><img src='transitions_heatmap_all.png' /></a></td>" >> $output
+echo "<td><a href='transitions_stacked_all.pdf'><img src='transitions_stacked_all.png' /></a></td>" >> $output
 echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
 echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
 first="true"
@@ -394,27 +395,27 @@
 
 if [ -e $outdir/aa_histogram.png ]
 then
-	echo "<img src='aa_histogram.png'/><br />" >> $output
+	echo "<a href='aa_histogram.pdf'><img src='aa_histogram.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGA.png ]
 then
-	echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGA.pdf'><img src='aa_histogram_IGA.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGG.png ]
 then
-	echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGG.pdf'><img src='aa_histogram_IGG.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGM.png ]
 then
-	echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGM.pdf'><img src='aa_histogram_IGM.png'/></a><br />" >> $output
 fi
 
 if [ -e $outdir/aa_histogram_IGE.png ]
 then
-	echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
+	echo "<a href='aa_histogram_IGE.pdf'><img src='aa_histogram_IGE.png'/></a><br />" >> $output
 fi
 
 
@@ -521,11 +522,11 @@
 
 if [ -e $outdir/IGA.png ] 
 then
-	echo "<img src='IGA.png'/><br />" >> $output
+	echo "<a href='IGA.pdf'><img src='IGA.png'/></a><br />" >> $output
 fi
 if [ -e $outdir/IGG.png ]
 then
-	echo "<img src='IGG.png'/><br />" >> $output
+	echo "<a href='IGG.pdf'><img src='IGG.png'/></a><br />" >> $output
 fi
 
 echo "<br />" >> $output