From 0aeafc05aafc73af04b116f373983caa655b08d5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 18 Mar 2020 07:38:44 -0500
Subject: [PATCH] Update intervene figure.
---
intervene_test/Intervene_results/Intervene_upset.R | 7 +++++++
.../Intervene_results/Intervene_upset_combinations.txt | 3 +++
intervene_test/intervene_figure.sh | 3 +--
3 files changed, 11 insertions(+), 2 deletions(-)
create mode 100755 intervene_test/Intervene_results/Intervene_upset.R
create mode 100644 intervene_test/Intervene_results/Intervene_upset_combinations.txt
diff --git a/intervene_test/Intervene_results/Intervene_upset.R b/intervene_test/Intervene_results/Intervene_upset.R
new file mode 100755
index 0000000..96a61e3
--- /dev/null
+++ b/intervene_test/Intervene_results/Intervene_upset.R
@@ -0,0 +1,7 @@
+#!/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())
diff --git a/intervene_test/Intervene_results/Intervene_upset_combinations.txt b/intervene_test/Intervene_results/Intervene_upset_combinations.txt
new file mode 100644
index 0000000..bdef8a0
--- /dev/null
+++ b/intervene_test/Intervene_results/Intervene_upset_combinations.txt
@@ -0,0 +1,3 @@
+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
diff --git a/intervene_test/intervene_figure.sh b/intervene_test/intervene_figure.sh
index 340b656..2eb227b 100644
--- a/intervene_test/intervene_figure.sh
+++ b/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
--
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