From 6a56e408fd615c56b361d0719448f9e860fce06a Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 7 Mar 2017 11:49:41 -0600
Subject: [PATCH] Verifyed that number of enhancers is 4974.
---
intervene_test/GRO-seq_enhancers.bed | 9963 ++++++++---------
intervene_test/Histone_barplot.png | Bin 13483 -> 13483 bytes
..._Shiny_App_genomic_UpSet_module_import.txt | 2 +-
.../intervene_genomic_UpSet_plot.R | 2 +-
.../intervene_genomic_UpSet_plot.pdf | Bin 6266 -> 6268 bytes
intervene_test/intervene_figure.sh | 6 +-
intervene_test/update_barplot.py | 2 +-
7 files changed, 4980 insertions(+), 4995 deletions(-)
diff --git a/intervene_test/GRO-seq_enhancers.bed b/intervene_test/GRO-seq_enhancers.bed
index a487b94..ece0f50 100644
--- a/intervene_test/GRO-seq_enhancers.bed
+++ b/intervene_test/GRO-seq_enhancers.bed
@@ -1,4989 +1,4974 @@
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+chrX 90299799 90300899 SSP_1061552
+chrX 91353599 91353749 SUNP_1472052
+chrX 91360299 91360399 SUNP_1472054
+chrX 91931199 91931799 SSP_1062128
+chrX 91931449 91932549 SSP_1062132
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+chrX 92934699 92935049 SUNP_1472925
+chrX 92934899 92935049 SUNP_1472927
+chrX 96891249 96891399 SUNP_1474886
+chrX 96891249 96891799 SUNP_1474887
+chrX 98371849 98371999 SSP_1066282
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+chrX 99283349 99283549 SSP_1066677
+chrX 100888699 100889199 SUNP_1476799
+chrX 101517499 101517699 SUNP_1477057
+chrX 102673499 102680249 SUNP_1477586
+chrX 102676249 102676699 SUNP_1477587
+chrX 102678549 102679449 SUNP_1477588
+chrX 102681799 102681949 SUNP_1477590
+chrX 102684599 102684749 SUNP_1477592
+chrX 103012549 103021349 SSP_1068959
+chrX 103015199 103015399 SSP_1068962
+chrX 103021399 103022699 SSP_1068975
+chrX 106740199 106745549 SSP_1070403
+chrX 108296049 108302549 SSP_1071073
+chrX 108297299 108301199 SSP_1071070
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+chrX 108297299 108301199 SSP_1071075
+chrX 108297299 108301199 SSP_1071074
+chrX 108297299 108302049 SSP_1071072
+chrX 110680199 110680649 SSP_1072074
+chrX 112199649 112200949 SSP_1073195
+chrX 112200699 112200949 SSP_1073199
+chrX 112200699 112200949 SSP_1073201
+chrX 113282599 113285049 SSP_1073500
+chrX 113282599 113285049 SSP_1073505
+chrX 113282599 113285049 SSP_1073503
+chrX 113283599 113283849 SSP_1073501
+chrX 113283599 113284699 SSP_1073502
+chrX 113283599 113284699 SSP_1073504
+chrX 113283599 113284749 SSP_1073506
+chrX 113293749 113295449 SSP_1073517
+chrX 113296049 113296449 SSP_1073520
+chrX 113296249 113298949 SSP_1073521
+chrX 113296249 113298949 SSP_1073522
+chrX 113703599 113703799 SSP_1073921
+chrX 113829699 113829849 SUNP_1483747
+chrX 113835749 113835849 SUNP_1483749
+chrX 114974249 114974399 SUNP_1484448
+chrX 114977249 114977699 SUNP_1484450
+chrX 114986349 114986499 SUNP_1484459
+chrX 114989349 114989499 SUNP_1484460
+chrX 114992399 114992549 SUNP_1484463
+chrX 114995349 114995499 SUNP_1484467
+chrX 114998299 114998449 SUNP_1484470
+chrX 115001299 115001449 SUNP_1484474
+chrX 115558649 115558999 SSP_1074966
+chrX 115558799 115558999 SSP_1074967
+chrX 116021099 116021349 SSP_1075282
+chrX 116420699 116420899 SSP_1075612
+chrX 116420699 116421149 SSP_1075613
+chrX 116420749 116420899 SSP_1075615
+chrX 120408999 120411999 SSP_1078438
+chrX 120409899 120411099 SSP_1078442
+chrX 120410749 120411099 SSP_1078444
+chrX 121102449 121111249 SSP_1079615
+chrX 121102449 121111249 SSP_1079618
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+chrX 121102449 121111249 SSP_1079613
+chrX 121102449 121111249 SSP_1079614
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+chrX 122184549 122186949 SSP_1080548
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+chrX 122184549 122186949 SSP_1080554
+chrX 122184699 122186749 SSP_1080549
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+chrX 132429699 132429799 SUNP_1493442
+chrX 132431499 132431649 SUNP_1493443
+chrX 136506899 136511949 SSP_1088697
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+chrX 137324299 137327349 SSP_1089876
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+chrY 3003699 3005949 SSP_1102019
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+chrY 3004799 3005749 SSP_1102024
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+chrY 3004799 3005749 SSP_1102023
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+chrY 4212349 4212999 SUNP_1506424
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+chrY 4391849 4393749 SSP_1102974
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+chrY 5190449 5190599 SUNP_1506907
+chrY 5193949 5194099 SUNP_1506909
+chrY 5505949 5506249 SUNP_1507119
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+chrY 6092299 6093499 SSP_1103778
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+chrY 9928949 9933499 SSP_1105613
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+chrY 13963049 13964149 SSP_1106439
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+chrY 14053899 14057449 SSP_1106543
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+chrY 14054749 14057449 SSP_1106545
+chrY 14054749 14057449 SSP_1106546
+chrY 14054749 14057499 SSP_1106548
+chrY 14054749 14059599 SSP_1106547
+chrY 15309699 15309849 SUNP_1509971
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+chrY 16292499 16292949 SSP_1108171
+chrY 17348999 17349499 SSP_1108715
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+chrY 17920899 17921049 SUNP_1511416
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diff --git a/intervene_test/Histone_barplot.png b/intervene_test/Histone_barplot.png
index 922372a1b974abe446db2db6ad66b7e7740e6c9c..93f2b82fd53034ff920b63c6453ccffc0d901cb2 100644
GIT binary patch
delta 2148
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delta 2150
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diff --git a/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt b/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
index b35ffed..6e8e1f3 100644
--- a/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
+++ b/intervene_test/Intervene_results/Intervene_Shiny_App_genomic_UpSet_module_import.txt
@@ -1,3 +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=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
diff --git a/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R b/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R
index 25c0f6a..bc29219 100755
--- a/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.R
+++ b/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())
diff --git a/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf b/intervene_test/Intervene_results/intervene_genomic_UpSet_plot.pdf
index 7703ab19db1e31dff555f43dda05c2c21d946928..78bc458548e12c2133c7dc24da4b8cf162425bbf 100644
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diff --git a/intervene_test/intervene_figure.sh b/intervene_test/intervene_figure.sh
index e789066..7cf1829 100644
--- a/intervene_test/intervene_figure.sh
+++ b/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"
diff --git a/intervene_test/update_barplot.py b/intervene_test/update_barplot.py
index ccc7674..c9c8cc6 100644
--- a/intervene_test/update_barplot.py
+++ b/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
--
GitLab