Mercurial > repos > pravs > protein_rna_correlation

diff protein_rna_correlation.r @ 6:8e9428eca82c draft

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planemo upload
author pravs
date Wed, 20 Jun 2018 21:09:54 -0400
parents 6bf0203ee17e
children 80892c607b1e
line wrap: on
line diff
--- a/protein_rna_correlation.r	Wed Jun 20 20:43:56 2018 -0400
+++ b/protein_rna_correlation.r	Wed Jun 20 21:09:54 2018 -0400
@@ -536,7 +536,8 @@
 #=============================================================================================================
 	cat("Generating Box and Density plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/AbundancePlot.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot, "png16m");
 	par(mfrow=c(2,2));
 	boxplot(proteome_df[,2], ylab="Abundance", main="Proteome abundance", cex.lab=1.5);
 	plot(density(proteome_df[,2]), xlab="Protein Abundance", ylab="Density", main="Proteome abundance", cex.lab=1.5);
@@ -554,7 +555,8 @@
 #=============================================================================================================
 	cat("Generating scatter plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/AbundancePlot_scatter.png",sep="",collapse="");
-	png(outplot);
+	#png(outplot);
+	bitmap(outplot,"png16m")
 	par(mfrow=c(1,1));
 	scatter.smooth(transcriptome_df[,2], proteome_df[,2], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5);	
 	
@@ -636,25 +638,29 @@
 	file = htmloutfile, append = TRUE);
 
 	outplot = paste(outdir,"/PE_GE_lm_1.png",sep="",collapse="");
-	png(outplot);
+	#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);
+	#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);
+	#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);
+	#png(outplot);
+	bitmap(outplot,"png16m");
 	par(mfrow=c(1,1));
 	plot(regmodel, 5, cex.lab=1.5);
 	dev.off();
@@ -705,7 +711,8 @@
 	
 	cat("Generating cooksd plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_lm_cooksd.png",sep="",collapse="");
-	png(outplot);
+	#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
@@ -765,7 +772,8 @@
 	# Scatter plot
 	#=============================================================================================================
 	outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse="");
-	png(outplot);
+	#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);	
 	
@@ -807,7 +815,8 @@
 	
 	cat("Generating heatmap plot\n",file=logfile, append=T);
 	outplot = paste(outdir,"/PE_GE_heatmap.png",sep="",collapse="");
-	png(outplot);
+	#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);
@@ -828,7 +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);
+	#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);