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 = "QRILC"
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': 'QRILC',
 'out_figures': PosixPath('runs/alzheimer_study/figures'),
 'out_folder': PosixPath('runs/alzheimer_study/diff_analysis/AD/PI_vs_QRILC'),
 '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_QRILC/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	QRILC
	var	SS	DF	F	p-unc	np2	-Log10 pvalue	qvalue	rejected
protein groups	Source
A0A024QZX5;A0A087X1N8;P35237	AD	0.741	1	4.819	0.029	0.025	1.532	0.075	False
	age	0.010	1	0.062	0.803	0.000	0.095	0.871	False
	Kiel	0.394	1	2.560	0.111	0.013	0.954	0.214	False
	Magdeburg	0.877	1	5.702	0.018	0.029	1.747	0.050	True
	Sweden	2.352	1	15.296	0.000	0.074	3.894	0.001	True
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	7.824	1	3.739	0.055	0.019	1.262	0.122	False
	age	0.011	1	0.005	0.941	0.000	0.026	0.965	False
	Kiel	6.913	1	3.303	0.071	0.017	1.150	0.150	False
	Magdeburg	21.543	1	10.294	0.002	0.051	2.805	0.006	True
	Sweden	0.048	1	0.023	0.879	0.000	0.056	0.926	False

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				QRILC
	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	0.029	1.532	0.075	False
	Kiel	0.045	1.347	0.112	False	0.111	0.954	0.214	False
	Magdeburg	0.005	2.274	0.020	True	0.018	1.747	0.050	True
	Sweden	0.000	3.574	0.002	True	0.000	3.894	0.001	True
	age	0.620	0.207	0.750	False	0.803	0.095	0.871	False
...	...	...	...	...	...	...	...	...	...
S4R3U6	AD	0.469	0.328	0.623	False	0.055	1.262	0.122	False
	Kiel	0.961	0.017	0.976	False	0.071	1.150	0.150	False
	Magdeburg	0.105	0.978	0.218	False	0.002	2.805	0.006	True
	Sweden	0.000	3.878	0.001	True	0.879	0.056	0.926	False
	age	0.185	0.734	0.328	False	0.941	0.026	0.965	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', 'QRILC': 'QRILC'}

Describe scores

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scores.describe()

model	PI			QRILC
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	0.244	2.748	0.310
std	0.303	5.328	0.331	0.296	5.185	0.323
min	0.000	0.000	0.000	0.000	0.000	0.000
25%	0.004	0.335	0.016	0.002	0.362	0.008
50%	0.121	0.916	0.243	0.092	1.035	0.185
75%	0.463	2.411	0.617	0.434	2.710	0.579
max	0.999	146.241	0.999	0.999	82.541	0.999

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_88988/3761369923.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				QRILC
	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	0.029	1.532	0.075	False
A0A024R0T9;K7ER74;P02655	AD	0.059	1.228	0.139	False	0.035	1.459	0.085	False
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	AD	0.040	1.393	0.103	False	0.305	0.516	0.454	False
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	AD	0.420	0.377	0.580	False	0.303	0.518	0.453	False
A0A075B6H7	AD	0.027	1.567	0.075	False	0.165	0.783	0.288	False
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	AD	0.175	0.756	0.316	False	0.175	0.756	0.302	False
Q9Y6X5	AD	0.070	1.155	0.159	False	0.101	0.994	0.199	False
Q9Y6Y8;Q9Y6Y8-2	AD	0.083	1.079	0.182	False	0.083	1.079	0.171	False
Q9Y6Y9	AD	0.348	0.459	0.512	False	0.832	0.080	0.891	False
S4R3U6	AD	0.469	0.328	0.623	False	0.055	1.262	0.122	False

1421 rows × 8 columns

And the descriptive statistics of the numeric values:

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scores.describe()

model	PI			QRILC
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	0.248	1.495	0.320
std	0.291	1.654	0.316	0.291	1.785	0.314
min	0.000	0.001	0.000	0.000	0.000	0.000
25%	0.013	0.368	0.041	0.009	0.365	0.028
50%	0.121	0.917	0.242	0.105	0.978	0.205
75%	0.428	1.899	0.588	0.431	2.046	0.576
max	0.999	25.104	0.999	0.999	25.180	0.999

and the boolean decision values

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

model	PI	QRILC
var	rejected	rejected
count	1421	1421
unique	2	2
top	False	False
freq	1031	999

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				QRILC				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	0.029	1.532	0.075	False	186
A0A024R0T9;K7ER74;P02655	0.059	1.228	0.139	False	0.035	1.459	0.085	False	195
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.040	1.393	0.103	False	0.305	0.516	0.454	False	174
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.420	0.377	0.580	False	0.303	0.518	0.453	False	196
A0A075B6H7	0.027	1.567	0.075	False	0.165	0.783	0.288	False	91
...	...	...	...	...	...	...	...	...	...
Q9Y6R7	0.175	0.756	0.316	False	0.175	0.756	0.302	False	197
Q9Y6X5	0.070	1.155	0.159	False	0.101	0.994	0.199	False	173
Q9Y6Y8;Q9Y6Y8-2	0.083	1.079	0.182	False	0.083	1.079	0.171	False	197
Q9Y6Y9	0.348	0.459	0.512	False	0.832	0.080	0.891	False	119
S4R3U6	0.469	0.328	0.623	False	0.055	1.262	0.122	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)  - QRILC (no)    965
PI (yes) - QRILC (yes)   356
PI (no)  - QRILC (yes)    66
PI (yes) - QRILC (no)     34
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_88988/1417621106.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				QRILC				data
	p-unc	-Log10 pvalue	qvalue	rejected	p-unc	-Log10 pvalue	qvalue	rejected	frequency
protein groups
A0A075B6I0	0.023	1.641	0.066	False	0.003	2.507	0.012	True	194
A0A087WWT2;Q9NPD7	0.034	1.470	0.090	False	0.005	2.335	0.016	True	193
A0A087X152;D6RE16;E0CX15;O95185;O95185-2	0.015	1.829	0.046	True	0.079	1.101	0.164	False	176
A0A0A0MTH0;Q8N0W4;Q8N0W4-2;Q8NFZ3;Q8NFZ3-2	0.110	0.959	0.225	False	0.017	1.763	0.048	True	189
A0A0A0MTP9;F8VZI9;Q9BWQ8	0.025	1.596	0.072	False	0.014	1.854	0.041	True	193
...	...	...	...	...	...	...	...	...	...
Q9P0K9	0.029	1.540	0.079	False	0.009	2.064	0.027	True	192
Q9UJ14	0.047	1.332	0.115	False	0.009	2.041	0.029	True	169
Q9UKB5	0.014	1.861	0.044	True	0.082	1.088	0.168	False	148
Q9UNW1	0.016	1.803	0.049	True	0.098	1.007	0.194	False	171
Q9UQ52	0.034	1.473	0.089	False	0.003	2.556	0.011	True	188

100 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	QRILC	frequency	Differential Analysis Comparison
protein groups
A0A024QZX5;A0A087X1N8;P35237	0.397	0.075	186	PI (no) - QRILC (no)
A0A024R0T9;K7ER74;P02655	0.139	0.085	195	PI (no) - QRILC (no)
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8	0.103	0.454	174	PI (no) - QRILC (no)
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503	0.580	0.453	196	PI (no) - QRILC (no)
A0A075B6H7	0.075	0.288	91	PI (no) - QRILC (no)
...	...	...	...	...
Q9Y6R7	0.316	0.302	197	PI (no) - QRILC (no)
Q9Y6X5	0.159	0.199	173	PI (no) - QRILC (no)
Q9Y6Y8;Q9Y6Y8-2	0.182	0.171	197	PI (no) - QRILC (no)
Q9Y6Y9	0.512	0.891	119	PI (no) - QRILC (no)
S4R3U6	0.623	0.122	126	PI (no) - QRILC (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	QRILC	frequency	Differential Analysis Comparison	diff_qvalue
protein groups
J3KSJ8;Q9UD71;Q9UD71-2	0.844	0.004	51	PI (no) - QRILC (yes)	0.840
E7EN89;E9PP67;E9PQ25;F2Z2Y8;Q9H0E2;Q9H0E2-2	0.821	0.016	86	PI (no) - QRILC (yes)	0.806
P43004;P43004-2;P43004-3	0.558	0.030	89	PI (no) - QRILC (yes)	0.528
A0A1W2PQ94;B4DS77;B4DS77-2;B4DS77-3	0.499	0.015	69	PI (no) - QRILC (yes)	0.484
F6SYF8;Q9UBP4	0.426	0.006	196	PI (no) - QRILC (yes)	0.420
...	...	...	...	...	...
P04080	0.058	0.040	143	PI (no) - QRILC (yes)	0.018
Q8IUK8	0.058	0.045	191	PI (no) - QRILC (yes)	0.013
K7ERI9;P02654	0.042	0.051	196	PI (yes) - QRILC (no)	0.009
P00740;P00740-2	0.053	0.048	197	PI (no) - QRILC (yes)	0.004
K7ERG9;P00746	0.052	0.048	197	PI (no) - QRILC (yes)	0.004

100 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_QRILC/diff_analysis_comparision_1_QRILC

• 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_QRILC/diff_analysis_comparision_2_QRILC

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