From 9ad9fcd7dabaaf982d3f7f5e949fdcddb2807380 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Thu, 23 Mar 2017 12:48:11 -0500
Subject: [PATCH] Added analysis of looking at Cluster 3.

---
 .../box_plot_cluster_3_enhancers_rpkm.png     | Bin 0 -> 12757 bytes
 GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png | Bin 0 -> 13218 bytes
 GRO_seq_TFSEE/matrix_analysis.py              | 140 +++++++++++++++++-
 3 files changed, 138 insertions(+), 2 deletions(-)
 create mode 100644 GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png
 create mode 100644 GRO_seq_TFSEE/box_plot_cluster_3_tfs_fpkm.png

diff --git a/GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png b/GRO_seq_TFSEE/box_plot_cluster_3_enhancers_rpkm.png
new file mode 100644
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HcmV?d00001

diff --git a/GRO_seq_TFSEE/matrix_analysis.py b/GRO_seq_TFSEE/matrix_analysis.py
index 141d502..d15ca83 100644
--- a/GRO_seq_TFSEE/matrix_analysis.py
+++ b/GRO_seq_TFSEE/matrix_analysis.py
@@ -518,10 +518,146 @@ plt.clf()
 
 
 # Wilcox rank sum test:
+# Cluster 1 1 e-5
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D0'],cell_tf_values_std_cluster_1['ES_D2'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D0'],cell_tf_values_std_cluster_1['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D0'],cell_tf_values_std_cluster_1['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D0'],cell_tf_values_std_cluster_1['ES_D10'])
+
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D2'],cell_tf_values_std_cluster_1['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D2'],cell_tf_values_std_cluster_1['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D2'],cell_tf_values_std_cluster_1['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D5'],cell_tf_values_std_cluster_1['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D5'],cell_tf_values_std_cluster_1['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_1['ES_D7'],cell_tf_values_std_cluster_1['ES_D10'])
+
+
+# Cluster 2 1 e-5
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D0'],cell_tf_values_std_cluster_2['ES_D2'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D0'],cell_tf_values_std_cluster_2['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D0'],cell_tf_values_std_cluster_2['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D0'],cell_tf_values_std_cluster_2['ES_D10'])
+
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D2'],cell_tf_values_std_cluster_2['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D2'],cell_tf_values_std_cluster_2['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D2'],cell_tf_values_std_cluster_2['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D5'],cell_tf_values_std_cluster_2['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D5'],cell_tf_values_std_cluster_2['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_2['ES_D7'],cell_tf_values_std_cluster_2['ES_D10'])
+
+# Cluster 3 1 e-5
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D0'],cell_tf_values_std_cluster_3['ES_D2'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D0'],cell_tf_values_std_cluster_3['ES_D5'])
 scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D0'],cell_tf_values_std_cluster_3['ES_D7'])
 scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D0'],cell_tf_values_std_cluster_3['ES_D10'])
-scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D10'],cell_tf_values_std_cluster_3['ES_D7'])
-scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D0'],cell_tf_values_std_cluster_3['ES_D7'])
+
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D2'],cell_tf_values_std_cluster_3['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D2'],cell_tf_values_std_cluster_3['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D2'],cell_tf_values_std_cluster_3['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D5'],cell_tf_values_std_cluster_3['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D5'],cell_tf_values_std_cluster_3['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_3['ES_D7'],cell_tf_values_std_cluster_3['ES_D10'])
+
+# Cluster 4 1 e-5
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D0'],cell_tf_values_std_cluster_4['ES_D2'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D0'],cell_tf_values_std_cluster_4['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D0'],cell_tf_values_std_cluster_4['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D0'],cell_tf_values_std_cluster_4['ES_D10'])
+
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D2'],cell_tf_values_std_cluster_4['ES_D5'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D2'],cell_tf_values_std_cluster_4['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D2'],cell_tf_values_std_cluster_4['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D5'],cell_tf_values_std_cluster_4['ES_D7'])
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D5'],cell_tf_values_std_cluster_4['ES_D10'])
+
+scipy.stats.ranksums(cell_tf_values_std_cluster_4['ES_D7'],cell_tf_values_std_cluster_4['ES_D10'])
+
+
+# Look at Cluster 3 for expression of TF's
+cluster3_tfs = tf_cell_lines.loc[cell_tf_values_std_cluster_3.index.values]
+
+box = cluster3_tfs.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 = 3)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 3)
+
+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((-5,65))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_3_tfs_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster3_tfs['ES_D0'],cluster3_tfs['ES_D2'])
+scipy.stats.ranksums(cluster3_tfs['ES_D0'],cluster3_tfs['ES_D5'])
+scipy.stats.ranksums(cluster3_tfs['ES_D0'],cluster3_tfs['ES_D7'])
+scipy.stats.ranksums(cluster3_tfs['ES_D0'],cluster3_tfs['ES_D10'])
+
+
+scipy.stats.ranksums(cluster3_tfs['ES_D2'],cluster3_tfs['ES_D5'])
+scipy.stats.ranksums(cluster3_tfs['ES_D2'],cluster3_tfs['ES_D7'])
+scipy.stats.ranksums(cluster3_tfs['ES_D2'],cluster3_tfs['ES_D10'])
+
+scipy.stats.ranksums(cluster3_tfs['ES_D5'],cluster3_tfs['ES_D7'])
+scipy.stats.ranksums(cluster3_tfs['ES_D5'],cluster3_tfs['ES_D10'])
+
+scipy.stats.ranksums(cluster3_tfs['ES_D7'],cluster3_tfs['ES_D10'])
+
+
+
+
+cluster3_motifs = motif_enhancers.loc[cell_tf_values_std_cluster_3.index.values]
+cluster3_enhancers = only_rpkm_values.loc[cluster3_motifs.loc[:, (cluster3_motifs != 0).all(axis=0)].columns.values]
+
+box = cluster3_enhancers.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 = 3)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 3)
+
+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((-5,105))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_3_enhancers_rpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster3_enhancers['ES_D0'],cluster3_enhancers['ES_D2'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D0'],cluster3_enhancers['ES_D5'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D0'],cluster3_enhancers['ES_D7'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D0'],cluster3_enhancers['ES_D10'])
+
+
+scipy.stats.ranksums(cluster3_enhancers['ES_D2'],cluster3_enhancers['ES_D5'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D2'],cluster3_enhancers['ES_D7'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D2'],cluster3_enhancers['ES_D10'])
+
+scipy.stats.ranksums(cluster3_enhancers['ES_D5'],cluster3_enhancers['ES_D7'])
+scipy.stats.ranksums(cluster3_enhancers['ES_D5'],cluster3_enhancers['ES_D10'])
+
+scipy.stats.ranksums(cluster3_enhancers['ES_D7'],cluster3_enhancers['ES_D10'])
+
+
 
 ## Analysis of only RNA-seq
 # 1. Z-score Standardize for each cell line to see important TF's
-- 
GitLab