From 0ca1b12c92be3e8f11aa97b5e299484428aa4e7f Mon Sep 17 00:00:00 2001
From: mlmial <ml.miale@icloud.com>
Date: Mon, 7 Aug 2023 00:06:00 +0200
Subject: [PATCH] edited seed variation plots
---
.../seed_variation_script.py | 75 +++++++++----------
1 file changed, 35 insertions(+), 40 deletions(-)
diff --git a/cami_src/evaluation_scripts/seed_variation_script.py b/cami_src/evaluation_scripts/seed_variation_script.py
index 3f24ee9..0ae2af9 100644
--- a/cami_src/evaluation_scripts/seed_variation_script.py
+++ b/cami_src/evaluation_scripts/seed_variation_script.py
@@ -52,15 +52,13 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
for tool in prediction_tools:
res_table.write(f'\t{tool}_msr_ks_pvalue')
- # if relevance scores file exsits:
- if os.path.exists(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)')):
- with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)'), 'r') as f:
- for line in f:
- val_name = line.split('\t')[0]
- redisc_table.write(f'\t{val_name}')
+ # with open(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{cami.uid}_relevance_scores.tsv'), 'r') as f:
+ # for line in f:
+ # val_name = line.split('\t')[0]
+ # res_table.write(f'\t{val_name}')
res_table.write('\n')
- # result dictionaries of the form {tool:list(value for each iteration)}
+ #result dictionaries of the form {tool:list(value for each iteration)}
tp_rate_dict = {k:list() for k in used_tools}
redisc_rate_dict = {k:list() for k in used_tools}
module_size_dict = {k:list() for k in used_tools}
@@ -89,11 +87,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
# reinitialize tools
cami.initialize_all_tools()
- # repeat consensus
- if ident%20==0:
- predict_and_make_consensus(cami)
- else:
- predict_and_make_consensus(cami)
+ predict_and_make_consensus(cami)
used_seeds = [cami.ppi_vertex2gene[seed] for seed in cami.seed_lst]
@@ -143,11 +137,11 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
p_val = kolmogorov_smirnoff.calculate_ks_p_value(list(module_size_dict[tool]),
list(module_size_dict[pred_tool]))
res_table.write(f'\t{p_val}')
- if os.path.exists(os.path.join(cami.tmp_dir, f'{used_tools[0]}_{identifier}_relevance_scores.tsv)')):
- with open(os.path.join(cami.tmp_dir, f'{tool}_{identifier}_relevance_scores.tsv'), 'r') as f:
- for line in f:
- rel_score = line.split('\t')[1].strip()
- res_table.write(f'\t{rel_score}')
+
+ #with open(os.path.join(cami.tmp_dir, f'{tool}_{identifier}_relevance_scores.tsv'), 'r') as f:
+ # for line in f:
+ # rel_score = line.split('\t')[1].strip()
+ # res_table.write(f'\t{rel_score}')
res_table.write('\n')
print(f'Result tables are saved in the following locations:')
@@ -168,12 +162,13 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
if second_occurrence_index > -1:
# replace the character at that index with the replacement character
tool_name = tool[:second_occurrence_index] + '\n' + tool[second_occurrence_index + 1:]
+ tool_name = tool_name.replace('_hub_penalty', '').replace('damping_factor', 'df').replace('confidence_level', 'cl').replace('ranking_trustrank', 'tr')
tool_labels[idx] = tool_name
if plot:
#PLOT
# Create a figure instance
#print(sys.getrecursionlimit())
- fig1, (ax1, ax5, ax4) = plt.subplots(3, 1, figsize=(20,20))
+ fig1, (ax1, ax5) = plt.subplots(2, 1, figsize=(12,12))
fig1.subplots_adjust(left=0.2)
# Extract Figure and Axes instance
@@ -186,7 +181,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
for violin, tool in zip(violins1['bodies'], tools):
if tool in [tw.name for tw in cami.tool_wrappers]:
violin.set_facecolor('saddlebrown')
- elif tool == 'first_neighbors':
+ elif tool == 'first_neighbours':
violin.set_facecolor('orange')
elif tool in ['union', 'intersection']:
violin.set_facecolor('peachpuff')
@@ -194,7 +189,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
violin.set_facecolor('red')
# Add title
- ax1.set_title(f'Rediscovery rate after randomly removing {nof_removals} seeds {nof_iterations} times from {identifier} seeds.', wrap=True, fontsize=14)
+ ax1.set_title(f'Rediscovery rate after randomly removing {nof_removals} seeds {nof_iterations} times\nfrom {identifier} seeds.', wrap=True, fontsize=14)
ax1.set_xticks(list(range(1,len(tools)+1)))
ax1.set_xticklabels(tool_labels)
@@ -202,26 +197,26 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
ax1.set_ylabel('Rediscovery rate (<rediscovered seeds>/<removed seeds>)', wrap=True, fontsize=14)
- violins2 = ax4.violinplot([tp_rate_dict[tool] for tool in tools], showmeans=True, showextrema=True)
- for violinpart in list(violins2.keys())[2:]:
- violins2[violinpart].set_color('k')
- for violin, tool in zip(violins2['bodies'], tools):
- if tool in [tw.name for tw in cami.tool_wrappers]:
- violin.set_facecolor('tan')
- elif tool == 'first_neighbors':
- violin.set_facecolor('peachpuff')
- elif tool in ['union', 'intersection']:
- violin.set_facecolor('orange')
- else:
- violin.set_facecolor('darkorange')
- # Add title
- ax4.set_title(f'True positive rates after randomly removing {nof_removals} seeds {nof_iterations} times from {identifier} seeds.', wrap=True, fontsize=14)
+ # violins2 = ax4.violinplot([tp_rate_dict[tool] for tool in tools], showmeans=True, showextrema=True)
+ # for violinpart in list(violins2.keys())[2:]:
+ # violins2[violinpart].set_color('k')
+ # for violin, tool in zip(violins2['bodies'], tools):
+ # if tool in [tw.name for tw in cami.tool_wrappers]:
+ # violin.set_facecolor('tan')
+ # elif tool == 'first_neighbors':
+ # violin.set_facecolor('peachpuff')
+ # elif tool in ['union', 'intersection']:
+ # violin.set_facecolor('orange')
+ # else:
+ # violin.set_facecolor('darkorange')
+ # # Add title
+ # ax4.set_title(f'True positive rates after randomly removing {nof_removals} seeds {nof_iterations} times from {identifier} seeds.', wrap=True, fontsize=14)
- ax4.set_xticks(list(range(1,len(tools)+1)))
- ax4.set_xticklabels(tool_labels)
- ax4.tick_params(axis='x', labelsize=11)
+ # ax4.set_xticks(list(range(1,len(tools)+1)))
+ # ax4.set_xticklabels(tool_labels)
+ # ax4.tick_params(axis='x', labelsize=11)
- ax4.set_ylabel('Sensitivity (TP/TP + FN)', wrap=True, fontsize=14)
+ # ax4.set_ylabel('Sensitivity (TP/TP + FN)', wrap=True, fontsize=14)
violins3 = ax5.violinplot([module_size_dict[tool] for tool in tools], showmeans=True, showextrema=True)
# Add title
@@ -231,14 +226,14 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Tru
for violin, tool in zip(violins3['bodies'], tools):
if tool in [tw.name for tw in cami.tool_wrappers]:
violin.set_facecolor('midnightblue')
- elif tool == 'first_neighbors':
+ elif tool == 'first_neighbours':
violin.set_facecolor('mediumblue')
elif tool in ['union', 'intersection']:
violin.set_facecolor('lightsteelblue')
else:
violin.set_facecolor('royalblue')
- ax5.set_title(f'Ratio of number of rediscovered seeds and predicted module size after removing {nof_removals} seeds {nof_iterations} times from {identifier} seeds.', wrap=True, fontsize=14)
+ ax5.set_title(f'Rediscovery module size ratio after removing {nof_removals} seeds {nof_iterations} times\nfrom {identifier} seeds.', wrap=True, fontsize=14)
ax5.set_xticks(list(range(1,len(tools)+1)))
ax5.set_xticklabels(tool_labels)
--
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