--- a/ChipSeqRatioAnalysis.R	Fri Nov 22 07:56:48 2019 -0500
+++ b/ChipSeqRatioAnalysis.R	Mon Dec 02 03:45:28 2019 -0500
@@ -53,7 +53,7 @@
 png(pngfile, width = 1000, height = 1200, pointsize=20)
 par(mfrow=c(2,1))
 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
-suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Seq ratio", pch=20, ylim=lims))
+suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims))
 abline(h=1,col='#00000080', lwd = 2)
 abline(h=2,col='#FF000080', lwd = 2)
 
@@ -82,5 +82,6 @@
        row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top")
 }
 HTMLEndFile(filename) 
-file.rename(from=filename, to=HTMLfile)
+# file.rename(from=filename, to=HTMLfile)
+system(sprintf("cp -r ./%s %s", filename, HTMLfile))
 write.table(df, file=input, sep="\t", row.names = FALSE)