Verifyed that number of enhancers is 4974.

intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt

 You can go to Intervene Shiny App https://asntech.shinyapps.io/Intervene-app/ and copy/paste the following intersection data to get more interactive figures.
 
-H3K27ac_enhancers=12510,H3K27ac_enhancers&H3K4me1_enhancers=55566,H3K4me1_enhancers=153327,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=610,GRO-seq_enhancers&H3K27ac_enhancers=256,GRO-seq_enhancers=3765,GRO-seq_enhancers&H3K4me1_enhancers=358
\ No newline at end of file
+H3K27ac_enhancers=12510,H3K27ac_enhancers&H3K4me1_enhancers=55566,H3K4me1_enhancers=153327,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=609,GRO-seq_enhancers&H3K27ac_enhancers=254,GRO-seq_enhancers=3754,GRO-seq_enhancers&H3K4me1_enhancers=357
\ No newline at end of file

intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R

@@ -2,6 +2,6 @@
 if (suppressMessages(!require("UpSetR"))) suppressMessages(install.packages("UpSetR", repos="http://cran.us.r-project.org"))
 library("UpSetR")
 pdf("/Users/venkatmalladi/Projects/PITTED/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf", width=10, height=8, onefile=FALSE)
-expressionInput <- c('H3K27ac_enhancers'=12510,'H3K27ac_enhancers&H3K4me1_enhancers'=55566,'H3K4me1_enhancers'=153327,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=610,'GRO-seq_enhancers&H3K27ac_enhancers'=256,'GRO-seq_enhancers'=3765,'GRO-seq_enhancers&H3K4me1_enhancers'=358)
+expressionInput <- c('H3K27ac_enhancers'=12510,'H3K27ac_enhancers&H3K4me1_enhancers'=55566,'H3K4me1_enhancers'=153327,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=609,'GRO-seq_enhancers&H3K27ac_enhancers'=254,'GRO-seq_enhancers'=3754,'GRO-seq_enhancers&H3K4me1_enhancers'=357)
 upset(fromExpression(expressionInput), nsets=3, nintersects=30, show.numbers="yes", main.bar.color="#108DCC", sets.bar.color="#E62128", empty.intersections=NULL, order.by = "degree", number.angles = 0, mainbar.y.label ="No. of Intersections", sets.x.label ="No. of Unique Enhancers")
 invisible(dev.off())

intervene_test/intervene_figure.sh

@@ -5,9 +5,9 @@ cp ../H3K4me1_filtered_peaks.bed H3K4me1_enhancers.bed
 cp ../H3K27ac_filtered_peaks.bed H3K27ac_enhancers.bed
 cp  ../SUNP_filtered_peaks.bed .
 cp  ../SSP_filtered_peaks_merged.bed .
-cut -f1,2,3  SUNP_filtered_peaks.bed > t
-cut -f1,2,3 SSP_filtered_peaks_merged.bed >> t
-sort-bed t > GRO-seq_enhancers.bed
+cut -f1,2,3,4  ../SUNP_filtered_peaks.bed > t
+cut -f1,2,3,4 ../SSP_filtered_peaks_merged.bed >> t
+sort-bed t | uniq > GRO-seq_enhancers.bed
 
 intervene upset -i *enhancers.bed --filename --order degree  --sxlabel "No. of Unique Enhancers" --dpi 1200  --figsize 10 8 --mbcolor "#108DCC"  --sbcolor "#E62128"
 

intervene_test/update_barplot.py

@@ -9,7 +9,7 @@ pts = np.array([
     179, 49, 189, 55720, 907, 12592, 153356])
 
 df = pd.DataFrame([
-    610, 256, 358, 55566, 3765, 12510, 153327])
+    609, 254, 357, 55566, 3754, 12510, 153327])
 
 ind = np.arange(N)  # the x locations for the groups
 width = 0.35       # the width of the bars