diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py
index ac95c15a9804d9147078540a2c557d36c6d1a7d4..70c1391e3bbe6d7fb210e1beea0bc99adafabebc 100644
--- a/cami_src/cami_suite.py
+++ b/cami_src/cami_suite.py
@@ -359,8 +359,8 @@ class cami():
for tool in result_sets:
result_sets[tool] -= set(self.seed_lst)
- params_1 = {'consens_threshold': [consens_threshold],
- 'function': {'cami_v1': cami_v1.run_cami}}
+ #params_1 = {'consens_threshold': [consens_threshold],
+ # 'function': {'cami_v1': cami_v1.run_cami}}
params_0 = {'function': {'union':cami_v1.make_union,
'intersection':cami_v1.make_intersection,
@@ -369,22 +369,15 @@ class cami():
params_tr1 = {'hub_penalty': [0.5],
'damping_factor': [0.85],
- 'confidence_level': [0.2, 0.5],
+ 'confidence_level': [0.2],
'ranking': ['trustrank'],
'function': {'cami_v2': cami_v2.run_cami}}
params_tr2 = {'hub_penalty': [0.5],
- 'damping_factor': [0.85, 0.75],
- 'confidence_level': [0.2, 0.35],
- 'ranking': ['trustrank'],
- 'function': {'cami_v3': cami_v3.run_cami}
- }
-
- params_tr3 = {'hub_penalty': [0.5],
- 'damping_factor': [0.1, 0.25],
+ 'damping_factor': [0.75],
'confidence_level': [0.2],
'ranking': ['trustrank'],
- 'function': {'cami_v2': cami_v2.run_cami}
+ 'function': {'cami_v3': cami_v3.run_cami}
}
# best for each disease set
@@ -436,17 +429,16 @@ class cami():
# 'cami_v3':cami_v3.run_cami}}
cami_setting_list = generate_param_combinations(params_0)+\
- generate_param_combinations(params_1)+\
generate_param_combinations(params_tr1)+\
- generate_param_combinations(params_tr2)+\
- generate_param_combinations(params_tr3)#+\
+ generate_param_combinations(params_tr2)#+\
+ # generate_param_combinations(params_tr3)#+\
# generate_param_combinations(params_tr4)#+\
# generate_param_combinations(params_tr5)
#generate_param_combinations(params_b_m)
camis = {}
for setting in cami_setting_list:
if setting[1]:
- func_name = setting[0] + '_' +setting[1]
+ func_name = setting[0]
else:
func_name = setting[0]
@@ -574,10 +566,11 @@ class cami():
Returns the URL of the result.
"""
# visualize with degradome
- n_venns = len(self.result_gene_sets)
+ n_venn_sets = {k:self.result_gene_sets[k] for k in self.result_gene_sets if k not in ['intersection', 'union', 'first_neighbours']}
+ n_venns = len(n_venn_sets)
if n_venns < 7:
degradome_sets = {tool: self.result_gene_sets[tool]
- for tool in self.result_gene_sets
+ for tool in n_venn_sets
if len(self.result_gene_sets[tool]) > 0}
url = degradome.send_request(degradome_sets)
with open(f'{self.output_dir}/venn_link_{self.uid}.txt', 'w') as f:
diff --git a/cami_src/evaluation_scripts/seed_variation_script.py b/cami_src/evaluation_scripts/seed_variation_script.py
index c3d41e959665cae0e97484ed9e8778324a67678c..0ae2af9325b79ea1130fd23671c2e7ffafeb87ac 100644
--- a/cami_src/evaluation_scripts/seed_variation_script.py
+++ b/cami_src/evaluation_scripts/seed_variation_script.py
@@ -17,7 +17,7 @@ def predict_and_make_consensus(cami, vis=False):
if vis:
cami.use_nvenn(download=True)
-def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=False):
+def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=True):
identifier = cami.uid
base_seeds = cami.origin_seed_lst
original_seeds = [cami.ppi_vertex2gene[seed] for seed in base_seeds]
@@ -52,10 +52,10 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
for tool in prediction_tools:
res_table.write(f'\t{tool}_msr_ks_pvalue')
- 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}')
+ # 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)}
@@ -138,10 +138,10 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
list(module_size_dict[pred_tool]))
res_table.write(f'\t{p_val}')
- 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:')
@@ -168,7 +168,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
#PLOT
# Create a figure instance
#print(sys.getrecursionlimit())
- fig1, (ax1, ax5) = plt.subplots(2, 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
@@ -181,7 +181,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
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')
@@ -189,7 +189,7 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
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)
@@ -226,14 +226,14 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
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)
@@ -244,4 +244,4 @@ def make_seedvariation(cami, n_iterations, removal_frac=0.2, vis=False, plot=Fal
fig1.savefig(f'{cami.output_dir}/00_{identifier}_seed_variation_result.png', bbox_inches="tight")
plt.close(fig1)
print(f'Violin plot saved under: 00_{identifier}_seed_variation_result.png')
- return cami
\ No newline at end of file
+ return cami