Use diff -u for the unified diff format. It’s easier to read. Lines prepended with a ‘-‘ disappeared going from file1 to file2, lines with a ‘+’ were added.

[alexx@macbook visualizations]$ diff -u seqDepth.old.R seqDepth.R
--- seqDepth.old.R	2013-12-19 11:19:36.120131845 +0100
+++ seqDepth.R	2013-12-19 11:18:26.426799353 +0100
@@ -8,13 +8,14 @@
 
 folder = "/s/project/coreProm"
 expDesign =  read.delim("/s/project/coreProm/tables/experimentDesign.txt")
-
 tables_folder <- file.path(folder, "tables", "TATA_box")
-##tables_folder <- file.path(folder, "tables", "single_TSS")
-##tables_folder <- file.path(folder, "tables")
-
 setwd(tables_folder)
 
+## <debug>
+tables_folder <- file.path(folder, "tables", "TATA_box")
+#tables_folder <- file.path(folder, "tables", "single_TSS")
+fi <- expDesign$filename[1]
+## </debug>
 
 tabs = lapply(
     expDesign$filename,
@@ -83,13 +84,13 @@
 
 }
 
-##png_em("promhead")
+png_em("promhead")
 
-##plot_em("promoter")
-##plot_em("head")
-##plot_em("body")
-##plot_em("tail")
-##plot_em("promhead")
+plot_em("promoter")
+plot_em("head")
+plot_em("body")
+plot_em("tail")
+plot_em("promhead")
 
 library(reshape2)
 mytab <- tab[,c(1, 2, 3, 8)]
@@ -125,11 +126,10 @@
 
 
 taf9_ecd <- subset(tab, TF=="TAF9" & condition=="Ecd_8h")
-tbp_ecd <-  subset(tab, TF=="TBP" & condition=="Ecd_8h")
 pol2_ecd <- subset(tab, TF=="PolII" & condition=="Ecd_8h")
 
 #plot(taf9_ecd$bod, pol2_ecd$promoter, log="xy")
-heatscatter(log10(tbp_ecd$head), log10(pol2_ecd$head))
+heatscatter(log10(taf9_ecd$head), log10(pol2_ecd$head))
 abline(0,1)
 lines(x=c(2, 2), y=c(0, 2))
 lines(x=c(0, 2), y=c(2, 2))