Overlap of enhancers plot.

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=12592,H3K27ac_enhancers&H3K4me1_enhancers=55720,H3K4me1_enhancers=153356,GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers=179,GRO-seq_enhancers&H3K27ac_enhancers=49,GRO-seq_enhancers=907,GRO-seq_enhancers&H3K4me1_enhancers=189
\ No newline at end of file

intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R

+#!/usr/bin/env Rscript
+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'=12592,'H3K27ac_enhancers&H3K4me1_enhancers'=55720,'H3K4me1_enhancers'=153356,'GRO-seq_enhancers&H3K27ac_enhancers&H3K4me1_enhancers'=179,'GRO-seq_enhancers&H3K27ac_enhancers'=49,'GRO-seq_enhancers'=907,'GRO-seq_enhancers&H3K4me1_enhancers'=189)
+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

+# Make overlap of enhancer data
+
+
+cp ../H3K4me1_filtered_peaks.bed H3K4me1_enhancers.bed
+cp ../H3K27ac_filtered_peaks.bed H3K27ac_enhancers.bed
+cp  ../SUNP_filtered_peaks.bed .
+cp  ../SUNP_filtered_peaks.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_filtered_peaks.bed
+
+intervene upset -i *enhancers.bed --filename --order degree  --sxlabel "No. of Unique Enhancers" --dpi 1200  --figsize 10 8 --mbcolor "#108DCC"  --sbcolor "#E62128"