Show cutoffs for H3K4me3 and H3K27ac marks.

cutoff_analysis.py

+#!/usr/bin/env python
+
+# -*- coding: latin-1 -*-
+'''Take an TSV file make a plot graph'''
+
+EPILOG = '''
+For more details:
+        %(prog)s --help
+'''
+
+
+import pandas as pd
+import matplotlib.pyplot as plt
+import numpy as np
+import argparse
+import seaborn as sns
+
+def get_args():
+    parser = argparse.ArgumentParser(
+            description=__doc__, epilog=EPILOG,
+            formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument('-r', '--rpkm',
+    	help="The file with RPKM values.",
+        required = True)
+    parser.add_argument('-c','--color',
+    	help="The hex color to make the graph",
+        required = True)
+    parser.add_argument('-f','--factor',
+    	help="Factor that is being analyzed.",
+        required = True)
+    parser.add_argument('-l','--limit',
+    	help="The RPKM limit to plot",
+        type=int,
+        required = True)
+    args = parser.parse_args()
+    return args
+
+def main():
+    sns.set_style("white")
+    sns.set_style("ticks")
+
+    args = get_args()
+    rpkm_file = pd.read_csv(args.rpkm, sep='\t')
+
+    locations = np.array(rpkm_file['ES_D0'])
+    locations = np.append(locations, np.array(rpkm_file['ES_D2']))
+    locations = np.append(locations, np.array(rpkm_file['ES_D5']))
+    locations = np.append(locations, np.array(rpkm_file['ES_D7']))
+    locations = np.append(locations, np.array(rpkm_file['ES_D10']))
+
+    sns.kdeplot(np.log2(locations[locations !=0 ] + 0.00001),color=args.color)
+    sns.despine()
+    plt.axvline(np.log2(args.limit), color='black', linestyle='dashed', linewidth=1)
+    plt.savefig(args.factor + '_distribution.png')
+    plt.clf()
+
+
+if __name__ == '__main__':
+    main()

h3k27ac_processing.sh

@@ -42,3 +42,9 @@ bedtools intersect -a /Volumes/project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT
 
 # Get RPKM
 ./rpkm.py --peaks universe_enhancer_H3K27ac.bed --experiments h3k27ac_list.csv -f H3K27ac
+
+./rpkm.py --peaks universe_enhancer_H3K27ac.bed --experiments h3k27ac_list.csv -f H3K27ac_all --minimum 0
+
+
+# Graph cutoffs
+./cutoff_analysis.py --rpkm H3K27ac_all_filtered_peaks.tsv --color '#008D14' --factor H3K27ac -l 1

h3k4me3_processing.sh

@@ -35,3 +35,7 @@ rm /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe
 
 # Get RPKM
 ./rpkm.py --peaks /Volumes/project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/universe_peaks.merge.bed --experiments h3k4me3_list.csv -f H3K4me3
+./rpkm.py --peaks /Volumes/project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/universe_peaks.merge.bed --experiments h3k4me3_list.csv -f H3K4me3_all --minimum 0
+
+# Graph cutoffs
+./cutoff_analysis.py --rpkm H3K4me3_all_filtered_peaks.tsv --color '#FF7C21' --factor H3K4me3 -l 1