Update intervene figure.

intervene_test/Intervene_results/Intervene_upset.R

+#!/usr/bin/env Rscript
+if (suppressMessages(!require("UpSetR"))) suppressMessages(install.packages("UpSetR", repos="http://cran.us.r-project.org"))
+library("UpSetR")
+pdf("/work/BICF/s163035/pitted/intervene_test/Intervene_results/Intervene_upset.pdf", width=10, height=8, onefile=FALSE)
+expressionInput <- c('H3K27ac_enhancers&Histone_enhancers'=12510,'H3K27ac_enhancers&Histone_enhancers&GRO-seq_enhancers'=151,'GRO-seq_enhancers'=3754,'Histone_enhancers&GRO-seq_enhancers'=0,'Histone_enhancers'=0,'H3K27ac_enhancers&GRO-seq_enhancers'=0,'H3K27ac_enhancers'=0,'H3K4me1_enhancers&H3K27ac_enhancers&Histone_enhancers&GRO-seq_enhancers'=317,'H3K4me1_enhancers&H3K27ac_enhancers&Histone_enhancers'=54405,'H3K4me1_enhancers&H3K27ac_enhancers'=0,'H3K4me1_enhancers&H3K27ac_enhancers&GRO-seq_enhancers'=0,'H3K4me1_enhancers&Histone_enhancers'=153327,'H3K4me1_enhancers&Histone_enhancers&GRO-seq_enhancers'=211,'H3K4me1_enhancers&GRO-seq_enhancers'=0,'H3K4me1_enhancers'=0)
+upset(fromExpression(expressionInput), nsets=4, 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_results/Intervene_upset_combinations.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&Histone_enhancers=12510,H3K27ac_enhancers&Histone_enhancers&GRO-seq_enhancers=151,GRO-seq_enhancers=3754,Histone_enhancers&GRO-seq_enhancers=0,Histone_enhancers=0,H3K27ac_enhancers&GRO-seq_enhancers=0,H3K27ac_enhancers=0,H3K4me1_enhancers&H3K27ac_enhancers&Histone_enhancers&GRO-seq_enhancers=317,H3K4me1_enhancers&H3K27ac_enhancers&Histone_enhancers=54405,H3K4me1_enhancers&H3K27ac_enhancers=0,H3K4me1_enhancers&H3K27ac_enhancers&GRO-seq_enhancers=0,H3K4me1_enhancers&Histone_enhancers=153327,H3K4me1_enhancers&Histone_enhancers&GRO-seq_enhancers=211,H3K4me1_enhancers&GRO-seq_enhancers=0,H3K4me1_enhancers=0
\ No newline at end of file

intervene_test/intervene_figure.sh

@@ -10,8 +10,7 @@ cut -f1,2,3,4 ../SSP_filtered_peaks_merged.bed >> t
 sort-bed t | uniq > GRO-seq_enhancers.bed
 cp ../Histone_pe_filtered_peaks.bed Histone_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 upset -i H3K4me1_enhancers.bed Histone_enhancers.bed GRO-seq_enhancers.bed --filename --order degree  --sxlabel "No. of Unique Enhancers" --dpi 1200  --figsize 10 8 --mbcolor "#108DCC"  --sbcolor "#E62128"
 
 # All called example:
 chr18:46,445,713-46,491,500