From 0e8e488c2d5f5dd18197a9b3a1e8f6b6719d8a02 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Tue, 6 Jun 2017 14:09:40 -0500
Subject: [PATCH] Update Histone analysis.

---
 GRO_seq_TFSEE/rank_order.py                   |  51 +++++++
 .../box_plot_cluster_2_genes_fpkm.png         | Bin 0 -> 36056 bytes
 .../box_plot_cluster_3_genes_fpkm.png         | Bin 0 -> 36071 bytes
 Histone_TFSEE/closest_genes.py                | 124 ++++++++++++++++++
 Histone_TFSEE/closest_genes.sh                |   6 +
 5 files changed, 181 insertions(+)
 create mode 100644 Histone_TFSEE/box_plot_cluster_2_genes_fpkm.png
 create mode 100644 Histone_TFSEE/box_plot_cluster_3_genes_fpkm.png
 create mode 100644 Histone_TFSEE/closest_genes.py
 create mode 100644 Histone_TFSEE/closest_genes.sh

diff --git a/GRO_seq_TFSEE/rank_order.py b/GRO_seq_TFSEE/rank_order.py
index c55da37..d633ec2 100644
--- a/GRO_seq_TFSEE/rank_order.py
+++ b/GRO_seq_TFSEE/rank_order.py
@@ -59,3 +59,54 @@ plt.xlabel('Rank Order',fontsize=8, fontweight='bold')
 plt.ylabel('delta z',fontsize=8, fontweight='bold')
 plt.savefig('cluster3_enriched_tfs.png')
 plt.clf()
+
+tfsee_cluster2 = tfsee[tfsee['cluster'] == 1]
+
+
+tfsee_cluster2['early'] = tfsee_cluster2[['ES_D0','ES_D2','ES_D7','ES_D10']].mean(axis=1)
+tfsee_cluster2['late'] = tfsee_cluster2[['ES_D5']].mean(axis=1)
+tfsee_cluster2['diff'] = tfsee_cluster2['late'] - tfsee_cluster2['early']
+tfsee_cluster2['rank'] = tfsee_cluster2['diff'].rank()
+
+x = list(tfsee_cluster2['rank'])
+
+z = np.polyfit(tfsee_cluster2['rank'], tfsee_cluster2['diff'], 3)
+f = np.poly1d(z)
+x_new = np.linspace(1, 24, num=len(x)*10)
+
+
+plt.figure(figsize=(25,20))
+plt.plot(x_new, f(x_new), color = 'k', linewidth=4.0)
+plt.scatter(x=tfsee_cluster2['rank'], y=tfsee_cluster2['diff'], color='#C42555', s=600)
+plt.ylim([-0.5,3.0])
+plt.suptitle('GT TFS', fontsize=8, fontweight='bold')
+plt.xlabel('Rank Order',fontsize=8, fontweight='bold')
+plt.ylabel('delta z',fontsize=8, fontweight='bold')
+plt.savefig('cluster2_enriched_tfs.png')
+plt.clf()
+
+
+tfsee_cluster1 = tfsee[tfsee['cluster'] == 0]
+
+
+tfsee_cluster1['early'] = tfsee_cluster1[['ES_D0','ES_D2','ES_D7','ES_D10']].mean(axis=1)
+tfsee_cluster1['late'] = tfsee_cluster1[['ES_D5']].mean(axis=1)
+tfsee_cluster1['diff'] = tfsee_cluster1['early'] - tfsee_cluster1['late']
+tfsee_cluster1['rank'] = tfsee_cluster1['diff'].rank()
+
+x = list(tfsee_cluster1['rank'])
+
+z = np.polyfit(tfsee_cluster1['rank'], tfsee_cluster1['diff'], 3)
+f = np.poly1d(z)
+x_new = np.linspace(1, 64, num=len(x)*10)
+
+
+plt.figure(figsize=(25,20))
+plt.plot(x_new, f(x_new), color = 'k', linewidth=4.0)
+plt.scatter(x=tfsee_cluster1['rank'], y=tfsee_cluster1['diff'], color='#DACF5D', s=600)
+plt.ylim([-1.0,1.5])
+plt.suptitle('Not GT TFS', fontsize=8, fontweight='bold')
+plt.xlabel('Rank Order',fontsize=8, fontweight='bold')
+plt.ylabel('delta z',fontsize=8, fontweight='bold')
+plt.savefig('cluster1_enriched_tfs.png')
+plt.clf()
diff --git a/Histone_TFSEE/box_plot_cluster_2_genes_fpkm.png b/Histone_TFSEE/box_plot_cluster_2_genes_fpkm.png
new file mode 100644
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diff --git a/Histone_TFSEE/closest_genes.py b/Histone_TFSEE/closest_genes.py
new file mode 100644
index 0000000..9130809
--- /dev/null
+++ b/Histone_TFSEE/closest_genes.py
@@ -0,0 +1,124 @@
+import pandas as pd
+import numpy as np
+import csv
+import matplotlib.pyplot as plt
+import seaborn as sns
+import scipy
+
+# Find nearest genes
+
+# Grab TF FPKM levels
+fpkm = pd.read_table("rna.tsv")
+gene_names_mapping = pd.read_csv("../gencode.v19.annotation_protein_coding_ids.txt",names=['gene_id', 'symbol'])
+fpkm_symbol = fpkm.merge(gene_names_mapping)
+fpkm_symbol = fpkm.set_index(['gene_id'])
+
+# Enhancers
+enhancers_universe = pd.DataFrame.from_csv("Histone_pe_filtered_peaks.bed", sep="\t", header=None, index_col=3)
+
+
+
+
+# Read in cluster 3 enhancers
+cluster_3 = pd.DataFrame.from_csv("cluster_3_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 3
+enhancers_universe_cluster_3 = enhancers_universe.loc[cluster_3.index.values]
+enhancers_universe_cluster_3.to_csv("cluster_3_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_3_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster3_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=12, color='black')
+box = cluster3_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 12)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 12)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,70))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_3_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 0.05
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D5'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D5'],cluster3_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D7'],cluster3_genes_expressed['ES_D10'])
+
+
+
+# Read in cluster 2 enhancers
+cluster_2 = pd.DataFrame.from_csv("cluster_2_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 2
+enhancers_universe_cluster_2 = enhancers_universe.loc[cluster_2.index.values]
+enhancers_universe_cluster_2.to_csv("cluster_2_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_2_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster2_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=12, color='black')
+box = cluster2_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 12)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 12)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,70))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_2_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D5'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D5'],cluster2_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D7'],cluster2_genes_expressed['ES_D10'])
diff --git a/Histone_TFSEE/closest_genes.sh b/Histone_TFSEE/closest_genes.sh
new file mode 100644
index 0000000..517ce84
--- /dev/null
+++ b/Histone_TFSEE/closest_genes.sh
@@ -0,0 +1,6 @@
+#Closest genes Cluster 3
+bedtools sort -i cluster_3_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_3_genes.txt
+
+
+#Closest genes Cluster 2
+bedtools sort -i cluster_2_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_2_genes.txt
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