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 = "CF"
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': 'CF',
 'out_figures': PosixPath('runs/alzheimer_study/figures'),
 'out_folder': PosixPath('runs/alzheimer_study/diff_analysis/AD/PI_vs_CF'),
 '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_CF/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	0.261	1	0.456	0.501	0.002	0.301	0.653	False
	age	0.036	1	0.063	0.802	0.000	0.096	0.878	False
	Kiel	1.631	1	2.848	0.093	0.015	1.031	0.198	False
	Magdeburg	4.653	1	8.127	0.005	0.041	2.315	0.018	True
	Sweden	7.129	1	12.451	0.001	0.061	3.281	0.003	True
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	0.832	1	0.895	0.345	0.005	0.462	0.508	False
	age	0.017	1	0.019	0.891	0.000	0.050	0.934	False
	Kiel	0.472	1	0.508	0.477	0.003	0.322	0.630	False
	Magdeburg	1.695	1	1.824	0.178	0.009	0.749	0.320	False
	Sweden	13.108	1	14.110	0.000	0.069	3.640	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	CF
	var	SS	DF	F	p-unc	np2	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	1.012	1	7.458	0.007	0.038	2.161	0.020	True
	age	0.004	1	0.031	0.860	0.000	0.066	0.907	False
	Kiel	0.255	1	1.878	0.172	0.010	0.764	0.281	False
	Magdeburg	0.474	1	3.494	0.063	0.018	1.200	0.125	False
	Sweden	1.692	1	12.470	0.001	0.061	3.285	0.002	True
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	2.445	1	4.785	0.030	0.024	1.524	0.068	False
	age	0.628	1	1.230	0.269	0.006	0.571	0.396	False
	Kiel	2.680	1	5.244	0.023	0.027	1.636	0.055	False
	Magdeburg	3.155	1	6.174	0.014	0.031	1.859	0.035	True
	Sweden	17.285	1	33.831	0.000	0.150	7.603	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	CF				PI
	var	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.007	2.161	0.020	True	0.501	0.301	0.653	False
	Kiel	0.172	0.764	0.281	False	0.093	1.031	0.198	False
	Magdeburg	0.063	1.200	0.125	False	0.005	2.315	0.018	True
	Sweden	0.001	3.285	0.002	True	0.001	3.281	0.003	True
	age	0.860	0.066	0.907	False	0.802	0.096	0.878	False
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	0.030	1.524	0.068	False	0.345	0.462	0.508	False
	Kiel	0.023	1.636	0.055	False	0.477	0.322	0.630	False
	Magdeburg	0.014	1.859	0.035	True	0.178	0.749	0.320	False
	Sweden	0.000	7.603	0.000	True	0.000	3.640	0.001	True
	age	0.269	0.571	0.396	False	0.891	0.050	0.934	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)

{'CF': 'CF', 'PI': 'PI'}

Describe scores

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scores.describe()

model	CF			PI
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	0.225	3.249	0.279	0.260	2.484	0.337
std	0.293	6.151	0.319	0.301	5.376	0.329
min	0.000	0.000	0.000	0.000	0.000	0.000
25%	0.001	0.406	0.002	0.004	0.336	0.015
50%	0.061	1.212	0.123	0.123	0.909	0.247
75%	0.393	3.281	0.524	0.462	2.431	0.615
max	0.999	86.232	0.999	1.000	145.647	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_111432/3761369923.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	CF				PI
	var	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.007	2.161	0.020	True	0.501	0.301	0.653	False
A0A024R0T9;K7ER74;P02655	AD	0.038	1.416	0.084	False	0.035	1.458	0.092	False
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	AD	0.598	0.224	0.707	False	0.102	0.990	0.214	False
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	AD	0.259	0.587	0.385	False	0.620	0.208	0.747	False
A0A075B6H7	AD	0.008	2.072	0.023	True	0.063	1.202	0.146	False
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	AD	0.175	0.756	0.285	False	0.175	0.756	0.317	False
Q9Y6X5	AD	0.092	1.035	0.171	False	0.057	1.241	0.136	False
Q9Y6Y8;Q9Y6Y8-2	AD	0.083	1.079	0.158	False	0.083	1.079	0.183	False
Q9Y6Y9	AD	0.317	0.499	0.449	False	0.561	0.251	0.697	False
S4R3U6	AD	0.030	1.524	0.068	False	0.345	0.462	0.508	False

1421 rows × 8 columns

And the descriptive statistics of the numeric values:

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scores.describe()

model	CF			PI
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	0.230	1.630	0.290	0.253	1.409	0.335
std	0.289	1.856	0.312	0.291	1.643	0.316
min	0.000	0.000	0.000	0.000	0.001	0.000
25%	0.007	0.405	0.019	0.012	0.363	0.040
50%	0.080	1.095	0.153	0.121	0.916	0.243
75%	0.393	2.187	0.524	0.434	1.909	0.591
max	0.999	18.530	0.999	0.997	23.415	0.998

and the boolean decision values

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

model	CF	PI
var	rejected	rejected
count	1421	1421
unique	2	2
top	False	False
freq	932	1025

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

	CF				PI				data
	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected	frequency
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.007	2.161	0.020	True	0.501	0.301	0.653	False	186
A0A024R0T9;K7ER74;P02655	0.038	1.416	0.084	False	0.035	1.458	0.092	False	195
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.598	0.224	0.707	False	0.102	0.990	0.214	False	174
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.259	0.587	0.385	False	0.620	0.208	0.747	False	196
A0A075B6H7	0.008	2.072	0.023	True	0.063	1.202	0.146	False	91
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	0.175	0.756	0.285	False	0.175	0.756	0.317	False	197
Q9Y6X5	0.092	1.035	0.171	False	0.057	1.241	0.136	False	173
Q9Y6Y8;Q9Y6Y8-2	0.083	1.079	0.158	False	0.083	1.079	0.183	False	197
Q9Y6Y9	0.317	0.499	0.449	False	0.561	0.251	0.697	False	119
S4R3U6	0.030	1.524	0.068	False	0.345	0.462	0.508	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
CF (no)  - PI (no)    875
CF (yes) - PI (yes)   339
CF (yes) - PI (no)    150
CF (no)  - PI (yes)    57
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_111432/1417621106.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'.

	CF				PI				data
	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected	frequency
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.007	2.161	0.020	True	0.501	0.301	0.653	False	186
A0A075B6H7	0.008	2.072	0.023	True	0.063	1.202	0.146	False	91
A0A075B6I0	0.001	3.121	0.003	True	0.032	1.488	0.088	False	194
A0A075B6R2	0.001	2.933	0.004	True	0.755	0.122	0.846	False	164
A0A075B6S5	0.008	2.108	0.022	True	0.138	0.861	0.266	False	129
...	...	...	...	...	...	...	...	...	...
Q9ULP0-3;Q9ULP0-6	0.001	3.245	0.002	True	0.025	1.596	0.072	False	136
Q9ULZ9	0.027	1.566	0.063	False	0.000	3.693	0.001	True	171
Q9UP79	0.000	4.201	0.000	True	0.346	0.460	0.509	False	135
Q9UQ52	0.001	3.067	0.003	True	0.061	1.212	0.144	False	188
Q9Y281;Q9Y281-3	0.002	2.803	0.006	True	0.206	0.687	0.356	False	51

207 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

	CF	PI	frequency	Differential Analysis Comparison
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.020	0.653	186	CF (yes) - PI (no)
A0A024R0T9;K7ER74;P02655	0.084	0.092	195	CF (no) - PI (no)
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.707	0.214	174	CF (no) - PI (no)
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.385	0.747	196	CF (no) - PI (no)
A0A075B6H7	0.023	0.146	91	CF (yes) - PI (no)
...	...	...	...	...
Q9Y6R7	0.285	0.317	197	CF (no) - PI (no)
Q9Y6X5	0.171	0.136	173	CF (no) - PI (no)
Q9Y6Y8;Q9Y6Y8-2	0.158	0.183	197	CF (no) - PI (no)
Q9Y6Y9	0.449	0.697	119	CF (no) - PI (no)
S4R3U6	0.068	0.508	126	CF (no) - PI (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)

	CF	PI	frequency	Differential Analysis Comparison	diff_qvalue
protein groups
A0A075B7B8	0.001	0.982	57	CF (yes) - PI (no)	0.981
Q14165	0.995	0.019	133	CF (no) - PI (yes)	0.977
O15197;O15197-3	0.004	0.969	104	CF (yes) - PI (no)	0.965
Q8N9I0	0.029	0.981	141	CF (yes) - PI (no)	0.953
P22748	0.034	0.986	159	CF (yes) - PI (no)	0.952
...	...	...	...	...	...
Q9NX62	0.046	0.056	197	CF (yes) - PI (no)	0.010
P00740;P00740-2	0.043	0.053	197	CF (yes) - PI (no)	0.010
K7ERG9;P00746	0.042	0.052	197	CF (yes) - PI (no)	0.009
K7EIS2;K7EKV3;K7EM70;K7EQL9;Q9BSG5;Q9BSG5-2;Q9BSG5-3	0.048	0.056	71	CF (yes) - PI (no)	0.008
Q16706	0.050	0.049	195	CF (no) - PI (yes)	0.001

207 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_CF/diff_analysis_comparision_1_CF

• 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_CF/diff_analysis_comparision_2_CF

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
PSEN1	ENSP00000326366	5.000
APP	ENSP00000284981	5.000
PSEN2	ENSP00000355747	5.000
APOE	ENSP00000252486	5.000
TREM2	ENSP00000362205	4.825
...	...	...
CEP170B	ENSP00000404151	0.683
SMPDL3A	ENSP00000357425	0.683
ADAMTS10	ENSP00000471851	0.683
PPP3R2	ENSP00000498330	0.683
VAT1	ENSP00000347872	0.683

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:3755: 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