Compare outcomes from differential analysis based on different imputation methods

• load scores based on 10_1_ald_diff_analysis

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import logging
from pathlib import Path

import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from IPython.display import display

import pimmslearn
import pimmslearn.databases.diseases

logger = pimmslearn.logging.setup_nb_logger()

plt.rcParams['figure.figsize'] = (2, 2)
fontsize = 5
pimmslearn.plotting.make_large_descriptors(fontsize)
logging.getLogger('fontTools').setLevel(logging.ERROR)

# catch passed parameters
args = None
args = dict(globals()).keys()

Parameters

Default and set parameters for the notebook.

folder_experiment = 'runs/appl_ald_data/plasma/proteinGroups'

target = 'kleiner'
model_key = 'VAE'
baseline = 'RSN'
out_folder = 'diff_analysis'
selected_statistics = ['p-unc', '-Log10 pvalue', 'qvalue', 'rejected']

disease_ontology = 5082  # code from https://disease-ontology.org/
# split diseases notebook? Query gene names for proteins in file from uniprot?
annotaitons_gene_col = 'PG.Genes'

# Parameters
disease_ontology = 10652
folder_experiment = "runs/alzheimer_study"
target = "AD"
baseline = "PI"
model_key = "RF"
out_folder = "diff_analysis"
annotaitons_gene_col = "None"

Add set parameters to configuration

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params = pimmslearn.nb.get_params(args, globals=globals())
args = pimmslearn.nb.Config()
args.folder_experiment = Path(params["folder_experiment"])
args = pimmslearn.nb.add_default_paths(args,
                                 out_root=(
                                     args.folder_experiment
                                     / params["out_folder"]
                                     / params["target"]
                                     / f"{params['baseline']}_vs_{params['model_key']}"))
args.update_from_dict(params)
args.scores_folder = scores_folder = (args.folder_experiment
                                      / params["out_folder"]
                                      / params["target"]
                                      / 'scores')
args.freq_features_observed = args.folder_experiment / 'freq_features_observed.csv'
args

root - INFO     Removed from global namespace: folder_experiment
root - INFO     Removed from global namespace: target
root - INFO     Removed from global namespace: model_key
root - INFO     Removed from global namespace: baseline
root - INFO     Removed from global namespace: out_folder
root - INFO     Removed from global namespace: selected_statistics
root - INFO     Removed from global namespace: disease_ontology
root - INFO     Removed from global namespace: annotaitons_gene_col
root - INFO     Already set attribute: folder_experiment has value runs/alzheimer_study
root - INFO     Already set attribute: out_folder has value diff_analysis

{'annotaitons_gene_col': 'None',
 'baseline': 'PI',
 'data': PosixPath('runs/alzheimer_study/data'),
 'disease_ontology': 10652,
 'folder_experiment': PosixPath('runs/alzheimer_study'),
 'freq_features_observed': PosixPath('runs/alzheimer_study/freq_features_observed.csv'),
 'model_key': 'RF',
 'out_figures': PosixPath('runs/alzheimer_study/figures'),
 'out_folder': PosixPath('runs/alzheimer_study/diff_analysis/AD/PI_vs_RF'),
 'out_metrics': PosixPath('runs/alzheimer_study'),
 'out_models': PosixPath('runs/alzheimer_study'),
 'out_preds': PosixPath('runs/alzheimer_study/preds'),
 'scores_folder': PosixPath('runs/alzheimer_study/diff_analysis/AD/scores'),
 'selected_statistics': ['p-unc', '-Log10 pvalue', 'qvalue', 'rejected'],
 'target': 'AD'}

Excel file for exports

files_out = dict()
writer_args = dict(float_format='%.3f')

fname = args.out_folder / 'diff_analysis_compare_methods.xlsx'
files_out[fname.name] = fname
writer = pd.ExcelWriter(fname)
logger.info("Writing to excel file: %s", fname)

root - INFO     Writing to excel file: runs/alzheimer_study/diff_analysis/AD/PI_vs_RF/diff_analysis_compare_methods.xlsx

Load scores

Load baseline model scores

Show all statistics, later use selected statistics

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fname = args.scores_folder / f'diff_analysis_scores_{args.baseline}.pkl'
scores_baseline = pd.read_pickle(fname)
scores_baseline

	model	PI
	var	SS	DF	F	p-unc	np2	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.833	1	1.390	0.240	0.007	0.620	0.397	False
	age	0.147	1	0.246	0.620	0.001	0.207	0.750	False
	Kiel	2.439	1	4.072	0.045	0.021	1.347	0.112	False
	Magdeburg	4.762	1	7.949	0.005	0.040	2.274	0.020	True
	Sweden	8.268	1	13.800	0.000	0.067	3.574	0.002	True
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	0.531	1	0.525	0.469	0.003	0.328	0.623	False
	age	1.792	1	1.774	0.185	0.009	0.734	0.328	False
	Kiel	0.002	1	0.002	0.961	0.000	0.017	0.976	False
	Magdeburg	2.675	1	2.648	0.105	0.014	0.978	0.218	False
	Sweden	15.376	1	15.221	0.000	0.074	3.878	0.001	True

7105 rows × 8 columns

Load selected comparison model scores

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fname = args.scores_folder / f'diff_analysis_scores_{args.model_key}.pkl'
scores_model = pd.read_pickle(fname)
scores_model

	model	RF
	var	SS	DF	F	p-unc	np2	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	1.010	1	7.629	0.006	0.038	2.200	0.019	True
	age	0.002	1	0.017	0.896	0.000	0.048	0.934	False
	Kiel	0.206	1	1.559	0.213	0.008	0.671	0.339	False
	Magdeburg	0.388	1	2.933	0.088	0.015	1.053	0.169	False
	Sweden	1.521	1	11.489	0.001	0.057	3.070	0.003	True
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	1.041	1	2.252	0.135	0.012	0.869	0.238	False
	age	0.807	1	1.746	0.188	0.009	0.726	0.308	False
	Kiel	1.830	1	3.958	0.048	0.020	1.318	0.103	False
	Magdeburg	1.832	1	3.963	0.048	0.020	1.319	0.103	False
	Sweden	12.678	1	27.419	0.000	0.126	6.367	0.000	True

7105 rows × 8 columns

Combined scores

show only selected statistics for comparsion

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scores = scores_model.join(scores_baseline, how='outer')[[args.baseline, args.model_key]]
scores = scores.loc[:, pd.IndexSlice[scores.columns.levels[0].to_list(),
                                     args.selected_statistics]]
scores

	model	PI				RF
	var	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.240	0.620	0.397	False	0.006	2.200	0.019	True
	Kiel	0.045	1.347	0.112	False	0.213	0.671	0.339	False
	Magdeburg	0.005	2.274	0.020	True	0.088	1.053	0.169	False
	Sweden	0.000	3.574	0.002	True	0.001	3.070	0.003	True
	age	0.620	0.207	0.750	False	0.896	0.048	0.934	False
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	0.469	0.328	0.623	False	0.135	0.869	0.238	False
	Kiel	0.961	0.017	0.976	False	0.048	1.318	0.103	False
	Magdeburg	0.105	0.978	0.218	False	0.048	1.319	0.103	False
	Sweden	0.000	3.878	0.001	True	0.000	6.367	0.000	True
	age	0.185	0.734	0.328	False	0.188	0.726	0.308	False

7105 rows × 8 columns

Models in comparison (name mapping)

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models = pimmslearn.nb.Config.from_dict(
    pimmslearn.pandas.index_to_dict(scores.columns.get_level_values(0)))
vars(models)

{'PI': 'PI', 'RF': 'RF'}

Describe scores

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scores.describe()

model	PI			RF
var	p-unc	-Log10 pvalue	qvalue	p-unc	-Log10 pvalue	qvalue
count	7,105.000	7,105.000	7,105.000	7,105.000	7,105.000	7,105.000
mean	0.261	2.476	0.338	0.233	3.079	0.291
std	0.303	5.328	0.331	0.295	5.788	0.323
min	0.000	0.000	0.000	0.000	0.000	0.000
25%	0.004	0.335	0.016	0.001	0.388	0.003
50%	0.121	0.916	0.243	0.071	1.149	0.142
75%	0.463	2.411	0.617	0.409	3.086	0.546
max	0.999	146.241	0.999	1.000	84.835	1.000

One to one comparison of by feature:

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scores = scores.loc[pd.IndexSlice[:, args.target], :]
scores.to_excel(writer, 'scores', **writer_args)
scores

/tmp/ipykernel_88901/3761369923.py:2: FutureWarning: Starting with pandas version 3.0 all arguments of to_excel except for the argument 'excel_writer' will be keyword-only.
  scores.to_excel(writer, 'scores', **writer_args)

	model	PI				RF
	var	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.240	0.620	0.397	False	0.006	2.200	0.019	True
A0A024R0T9;K7ER74;P02655	AD	0.059	1.228	0.139	False	0.031	1.511	0.072	False
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	AD	0.040	1.393	0.103	False	0.403	0.395	0.540	False
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	AD	0.420	0.377	0.580	False	0.257	0.591	0.390	False
A0A075B6H7	AD	0.027	1.567	0.075	False	0.009	2.051	0.026	True
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	AD	0.175	0.756	0.316	False	0.175	0.756	0.292	False
Q9Y6X5	AD	0.070	1.155	0.159	False	0.203	0.692	0.327	False
Q9Y6Y8;Q9Y6Y8-2	AD	0.083	1.079	0.182	False	0.083	1.079	0.162	False
Q9Y6Y9	AD	0.348	0.459	0.512	False	0.328	0.484	0.468	False
S4R3U6	AD	0.469	0.328	0.623	False	0.135	0.869	0.238	False

1421 rows × 8 columns

And the descriptive statistics of the numeric values:

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scores.describe()

model	PI			RF
var	p-unc	-Log10 pvalue	qvalue	p-unc	-Log10 pvalue	qvalue
count	1,421.000	1,421.000	1,421.000	1,421.000	1,421.000	1,421.000
mean	0.252	1.411	0.334	0.246	1.519	0.311
std	0.291	1.654	0.316	0.293	1.759	0.317
min	0.000	0.001	0.000	0.000	0.001	0.000
25%	0.013	0.368	0.041	0.009	0.374	0.027
50%	0.121	0.917	0.242	0.101	0.997	0.188
75%	0.428	1.899	0.588	0.423	2.030	0.559
max	0.999	25.104	0.999	0.998	18.758	0.998

and the boolean decision values

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scores.describe(include=['bool', 'O'])

model	PI	RF
var	rejected	rejected
count	1421	1421
unique	2	2
top	False	False
freq	1031	961

Load frequencies of observed features

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freq_feat = pd.read_csv(args.freq_features_observed, index_col=0)
freq_feat.columns = pd.MultiIndex.from_tuples([('data', 'frequency'),])
freq_feat

	data
	frequency
protein groups
A0A024QZX5;A0A087X1N8;P35237	186
A0A024R0T9;K7ER74;P02655	195
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	174
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	196
A0A075B6H7	91
...	...
Q9Y6R7	197
Q9Y6X5	173
Q9Y6Y8;Q9Y6Y8-2	197
Q9Y6Y9	119
S4R3U6	126

1421 rows × 1 columns

Compare shared features

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scores_common = (scores
                 .dropna()
                 .reset_index(-1, drop=True)
                 ).join(
    freq_feat, how='left'
)
scores_common

	PI				RF				data
	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected	frequency
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.240	0.620	0.397	False	0.006	2.200	0.019	True	186
A0A024R0T9;K7ER74;P02655	0.059	1.228	0.139	False	0.031	1.511	0.072	False	195
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.040	1.393	0.103	False	0.403	0.395	0.540	False	174
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.420	0.377	0.580	False	0.257	0.591	0.390	False	196
A0A075B6H7	0.027	1.567	0.075	False	0.009	2.051	0.026	True	91
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	0.175	0.756	0.316	False	0.175	0.756	0.292	False	197
Q9Y6X5	0.070	1.155	0.159	False	0.203	0.692	0.327	False	173
Q9Y6Y8;Q9Y6Y8-2	0.083	1.079	0.182	False	0.083	1.079	0.162	False	197
Q9Y6Y9	0.348	0.459	0.512	False	0.328	0.484	0.468	False	119
S4R3U6	0.469	0.328	0.623	False	0.135	0.869	0.238	False	126

1421 rows × 9 columns

Annotate decisions in Confusion Table style:

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def annotate_decision(scores, model, model_column):
    return scores[(model_column, 'rejected')].replace({False: f'{model} (no) ', True: f'{model} (yes)'})


annotations = None
for model, model_column in models.items():
    if annotations is not None:
        annotations += ' - '
        annotations += annotate_decision(scores_common,
                                         model=model, model_column=model_column)
    else:
        annotations = annotate_decision(
            scores_common, model=model, model_column=model_column)
annotations.name = 'Differential Analysis Comparison'
annotations.value_counts()

Differential Analysis Comparison
PI (no)  - RF (no)    896
PI (yes) - RF (yes)   325
PI (no)  - RF (yes)   135
PI (yes) - RF (no)     65
Name: count, dtype: int64

List different decisions between models

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mask_different = (
    (scores_common.loc[:, pd.IndexSlice[:, 'rejected']].any(axis=1))
    & ~(scores_common.loc[:, pd.IndexSlice[:, 'rejected']].all(axis=1))
)
_to_write = scores_common.loc[mask_different]
_to_write.to_excel(writer, 'differences', **writer_args)
logger.info("Writen to Excel file under sheet 'differences'.")
_to_write

/tmp/ipykernel_88901/1417621106.py:6: FutureWarning: Starting with pandas version 3.0 all arguments of to_excel except for the argument 'excel_writer' will be keyword-only.
  _to_write.to_excel(writer, 'differences', **writer_args)
root - INFO     Writen to Excel file under sheet 'differences'.

	PI				RF				data
	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected	frequency
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.240	0.620	0.397	False	0.006	2.200	0.019	True	186
A0A075B6H7	0.027	1.567	0.075	False	0.009	2.051	0.026	True	91
A0A075B6I0	0.023	1.641	0.066	False	0.001	3.146	0.003	True	194
A0A075B6J9	0.028	1.552	0.077	False	0.019	1.713	0.049	True	156
A0A075B6R2	0.259	0.587	0.419	False	0.002	2.734	0.007	True	164
...	...	...	...	...	...	...	...	...	...
Q9UKB5	0.014	1.861	0.044	True	0.474	0.324	0.606	False	148
Q9ULZ9	0.003	2.460	0.014	True	0.071	1.150	0.142	False	171
Q9UNW1	0.016	1.803	0.049	True	0.920	0.036	0.950	False	171
Q9UP79	0.316	0.501	0.480	False	0.000	3.777	0.001	True	135
Q9UQ52	0.034	1.473	0.089	False	0.001	3.082	0.003	True	188

200 rows × 9 columns

Plot qvalues of both models with annotated decisions

Prepare data for plotting (qvalues)

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var = 'qvalue'
to_plot = [scores_common[v][var] for v in models.values()]
for s, k in zip(to_plot, models.keys()):
    s.name = k.replace('_', ' ')
to_plot.append(scores_common['data'])
to_plot.append(annotations)
to_plot = pd.concat(to_plot, axis=1)
to_plot

	PI	RF	frequency	Differential Analysis Comparison
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.397	0.019	186	PI (no) - RF (yes)
A0A024R0T9;K7ER74;P02655	0.139	0.072	195	PI (no) - RF (no)
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.103	0.540	174	PI (no) - RF (no)
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.580	0.390	196	PI (no) - RF (no)
A0A075B6H7	0.075	0.026	91	PI (no) - RF (yes)
...	...	...	...	...
Q9Y6R7	0.316	0.292	197	PI (no) - RF (no)
Q9Y6X5	0.159	0.327	173	PI (no) - RF (no)
Q9Y6Y8;Q9Y6Y8-2	0.182	0.162	197	PI (no) - RF (no)
Q9Y6Y9	0.512	0.468	119	PI (no) - RF (no)
S4R3U6	0.623	0.238	126	PI (no) - RF (no)

1421 rows × 4 columns

List of features with the highest difference in qvalues

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# should it be possible to run not only RSN?
to_plot['diff_qvalue'] = (to_plot[str(args.baseline)] - to_plot[str(args.model_key)]).abs()
to_plot.loc[mask_different].sort_values('diff_qvalue', ascending=False)

	PI	RF	frequency	Differential Analysis Comparison	diff_qvalue
protein groups
P55268	0.999	0.049	194	PI (no) - RF (yes)	0.949
F6VDH7;P50502;Q3KNR6	0.011	0.958	175	PI (yes) - RF (no)	0.946
P17302	0.942	0.002	135	PI (no) - RF (yes)	0.939
A0A087X1Z2;C9JTV4;H0Y4Y4;Q8WYH2;Q96C19;Q9BUP0;Q9BUP0-2	0.004	0.939	66	PI (yes) - RF (no)	0.935
A0A087WU43;A0A087WX17;A0A087WXI5;P12830;P12830-2	0.931	0.001	134	PI (no) - RF (yes)	0.929
...	...	...	...	...	...
O15354	0.059	0.050	197	PI (no) - RF (yes)	0.009
Q9NX62	0.056	0.047	197	PI (no) - RF (yes)	0.009
P00740;P00740-2	0.053	0.044	197	PI (no) - RF (yes)	0.008
K7ERG9;P00746	0.052	0.044	197	PI (no) - RF (yes)	0.008
Q16706	0.046	0.054	195	PI (yes) - RF (no)	0.008

200 rows × 5 columns

Differences plotted with created annotations

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figsize = (4, 4)
size = 5
fig, ax = plt.subplots(figsize=figsize)
x_col = to_plot.columns[0]
y_col = to_plot.columns[1]
ax = sns.scatterplot(data=to_plot,
                     x=x_col,
                     y=y_col,
                     s=size,
                     hue='Differential Analysis Comparison',
                     ax=ax)
_ = ax.legend(fontsize=fontsize,
              title_fontsize=fontsize,
              markerscale=0.4,
              title='',
              )
ax.set_xlabel(f"qvalue for {x_col}")
ax.set_ylabel(f"qvalue for {y_col}")
ax.hlines(0.05, 0, 1, color='grey', linestyles='dotted')
ax.vlines(0.05, 0, 1, color='grey', linestyles='dotted')
sns.move_legend(ax, "upper right")
files_out[f'diff_analysis_comparision_1_{args.model_key}'] = (
    args.out_folder /
    f'diff_analysis_comparision_1_{args.model_key}')
fname = files_out[f'diff_analysis_comparision_1_{args.model_key}']
pimmslearn.savefig(fig, name=fname)

pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/diff_analysis/AD/PI_vs_RF/diff_analysis_comparision_1_RF

• also showing how many features were measured (“observed”) by size of circle

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fig, ax = plt.subplots(figsize=figsize)
ax = sns.scatterplot(data=to_plot,
                     x=to_plot.columns[0],
                     y=to_plot.columns[1],
                     size='frequency',
                     s=size,
                     sizes=(5, 20),
                     hue='Differential Analysis Comparison')
_ = ax.legend(fontsize=fontsize,
              title_fontsize=fontsize,
              markerscale=0.6,
              title='',
              )
ax.set_xlabel(f"qvalue for {x_col}")
ax.set_ylabel(f"qvalue for {y_col}")
ax.hlines(0.05, 0, 1, color='grey', linestyles='dotted')
ax.vlines(0.05, 0, 1, color='grey', linestyles='dotted')
sns.move_legend(ax, "upper right")
files_out[f'diff_analysis_comparision_2_{args.model_key}'] = (
    args.out_folder / f'diff_analysis_comparision_2_{args.model_key}')
pimmslearn.savefig(
    fig, name=files_out[f'diff_analysis_comparision_2_{args.model_key}'])

pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/diff_analysis/AD/PI_vs_RF/diff_analysis_comparision_2_RF

Only features contained in model

• this block exist due to a specific part in the ALD analysis of the paper

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scores_model_only = scores.reset_index(level=-1, drop=True)
_diff = scores_model_only.index.difference(scores_common.index)
if not _diff.empty:
    scores_model_only = (scores_model_only
                         .loc[
                             _diff,
                             args.model_key]
                         .sort_values(by='qvalue', ascending=True)
                         .join(freq_feat.squeeze().rename(freq_feat.columns.droplevel()[0])
                               )
                         )
    display(scores_model_only)
else:
    scores_model_only = None
    logger.info("No features only in new comparision model.")

if not _diff.empty:
    scores_model_only.to_excel(writer, 'only_model', **writer_args)
    display(scores_model_only.rejected.value_counts())
    scores_model_only_rejected = scores_model_only.loc[scores_model_only.rejected]
    scores_model_only_rejected.to_excel(
        writer, 'only_model_rejected', **writer_args)

root - INFO     No features only in new comparision model.

DISEASES DB lookup

Query diseases database for gene associations with specified disease ontology id.

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data = pimmslearn.databases.diseases.get_disease_association(
    doid=args.disease_ontology, limit=10000)
data = pd.DataFrame.from_dict(data, orient='index').rename_axis('ENSP', axis=0)
data = data.rename(columns={'name': args.annotaitons_gene_col}).reset_index(
).set_index(args.annotaitons_gene_col)
data

pimmslearn.databases.diseases - WARNING  There are more associations available

	ENSP	score
None
APP	ENSP00000284981	5.000
PSEN2	ENSP00000355747	5.000
PSEN1	ENSP00000326366	5.000
APOE	ENSP00000252486	5.000
TREM2	ENSP00000362205	4.825
...	...	...
PTTG1	ENSP00000377536	0.682
ISL2	ENSP00000290759	0.682
hsa-miR-4433b-3p	hsa-miR-4433b-3p	0.682
NEURL1B	ENSP00000358815	0.681
SLC26A4	ENSP00000494017	0.681

10000 rows × 2 columns

Shared features

ToDo: new script -> DISEASES DB lookup

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feat_name = scores.index.names[0]  # first index level is feature name
if args.annotaitons_gene_col in scores.index.names:
    logger.info(f"Found gene annotation in scores index:  {scores.index.names}")
else:
    logger.info(f"No gene annotation in scores index:  {scores.index.names}"
                " Exiting.")
    import sys
    sys.exit(0)

root - INFO     No gene annotation in scores index:  ['protein groups', 'Source'] Exiting.
/home/runner/work/pimms/pimms/project/.snakemake/conda/43fbe714d68d8fe6f9b0c93f5652adb3_/lib/python3.12/site-packages/IPython/core/interactiveshell.py:3756: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.
  warn("To exit: use 'exit', 'quit', or Ctrl-D.", stacklevel=1)

An exception has occurred, use %tb to see the full traceback.

SystemExit: 0

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gene_to_PG = (scores.droplevel(
    list(set(scores.index.names) - {feat_name, args.annotaitons_gene_col})
)
    .index
    .to_frame()
    .reset_index(drop=True)
    .set_index(args.annotaitons_gene_col)
)
gene_to_PG.head()

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disease_associations_all = data.join(
    gene_to_PG).dropna().reset_index().set_index(feat_name).join(annotations)
disease_associations_all

only by model

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idx = disease_associations_all.index.intersection(scores_model_only.index)
disease_assocications_new = disease_associations_all.loc[idx].sort_values(
    'score', ascending=False)
disease_assocications_new.head(20)

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mask = disease_assocications_new.loc[idx, 'score'] >= 2.0
disease_assocications_new.loc[idx].loc[mask]

Only by model which were significant

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idx = disease_associations_all.index.intersection(
    scores_model_only_rejected.index)
disease_assocications_new_rejected = disease_associations_all.loc[idx].sort_values(
    'score', ascending=False)
disease_assocications_new_rejected.head(20)

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mask = disease_assocications_new_rejected.loc[idx, 'score'] >= 2.0
disease_assocications_new_rejected.loc[idx].loc[mask]

Shared which are only significant for by model

mask = (scores_common[(str(args.model_key), 'rejected')] & mask_different)
mask.sum()

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idx = disease_associations_all.index.intersection(mask.index[mask])
disease_assocications_shared_rejected_by_model = (disease_associations_all.loc[idx].sort_values(
    'score', ascending=False))
disease_assocications_shared_rejected_by_model.head(20)

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mask = disease_assocications_shared_rejected_by_model.loc[idx, 'score'] >= 2.0
disease_assocications_shared_rejected_by_model.loc[idx].loc[mask]

Only significant by RSN

mask = (scores_common[(str(args.baseline), 'rejected')] & mask_different)
mask.sum()

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idx = disease_associations_all.index.intersection(mask.index[mask])
disease_assocications_shared_rejected_by_RSN = (
    disease_associations_all
    .loc[idx]
    .sort_values('score', ascending=False))
disease_assocications_shared_rejected_by_RSN.head(20)

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mask = disease_assocications_shared_rejected_by_RSN.loc[idx, 'score'] >= 2.0
disease_assocications_shared_rejected_by_RSN.loc[idx].loc[mask]

Write to excel

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disease_associations_all.to_excel(
    writer, sheet_name='disease_assoc_all', **writer_args)
disease_assocications_new.to_excel(
    writer, sheet_name='disease_assoc_new', **writer_args)
disease_assocications_new_rejected.to_excel(
    writer, sheet_name='disease_assoc_new_rejected', **writer_args)

Outputs

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writer.close()
files_out