Mercurial > repos > pravs > protein_rna_correlation

diff protein_rna_correlation.r @ 8:80892c607b1e draft

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planemo upload
author pravs
date Wed, 20 Jun 2018 21:33:37 -0400
parents 8e9428eca82c
children e407b1a7a8de
line wrap: on
line diff
--- a/protein_rna_correlation.r	Wed Jun 20 21:23:00 2018 -0400
+++ b/protein_rna_correlation.r	Wed Jun 20 21:33:37 2018 -0400
@@ -638,29 +638,29 @@
 	file = htmloutfile, append = TRUE);
 
 	outplot = paste(outdir,"/PE_GE_lm_1.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 1, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_2.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 2, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_3.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 3, cex.lab=1.5);
 	dev.off();
 	
 	outplot = paste(outdir,"/PE_GE_lm_5.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 5, cex.lab=1.5);
 	dev.off();
@@ -711,8 +711,8 @@
 	
 	cat("Generating cooksd plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_lm_cooksd.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(cooksd, pch="*", cex=2, cex.lab=1.5,main="Influential Obs. by Cooks distance", ylab="Cook\'s distance", xlab="Observations")  # plot cooks distance
 	abline(h = 4*mean(cooksd, na.rm=T), col="red")  # add cutoff line
@@ -772,8 +772,8 @@
 	# Scatter plot
 	#=============================================================================================================
 	outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	scatter.smooth(PE_GE_data_no_outlier[,"GE_abundance"], PE_GE_data_no_outlier[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);	
 	
@@ -815,8 +815,8 @@
 	
 	cat("Generating heatmap plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_heatmap.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	#heatmap.2(as.matrix(PE_GE_data[,c("PE_abundance","GE_abundance")]), trace="none", cexCol=1, col=greenred(100),Colv=F, labCol=c("PE","GE"), scale="col");
 	my_palette <- colorRampPalette(c("green", "white", "red"))(299);
@@ -837,8 +837,8 @@
 	k1 = kmeans(PE_GE_data_kdata[,c("PE_abundance","GE_abundance")], 5);
 	cat("Generating kmeans plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_kmeans.png",sep="",collapse="");
-	#png(outplot);
-	bitmap(outplot,"png16m");
+	png(outplot);
+	#bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	scatter.smooth(PE_GE_data_kdata[,"GE_abundance"], PE_GE_data_kdata[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);