Differential Analysis - Compare model imputation with standard imputation

Differential Analysis - Compare model imputation with standard imputation#

  • load missing values predictions (if specified)

  • leave all other values as they were

  • compare missing values predicition by model with baseline method (default: draw from shifted normal distribution. short RSN)

Hide code cell source

 
import logging
from pathlib import Path

import matplotlib.pyplot as plt
import njab.stats
import pandas as pd
from IPython.display import display

import pimmslearn
import pimmslearn.analyzers
import pimmslearn.imputation
import pimmslearn.io.datasplits
import pimmslearn.nb

logger = pimmslearn.logging.setup_nb_logger()
logging.getLogger('fontTools').setLevel(logging.WARNING)

Hide code cell source

 
# 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"
folder_data: str = ''  # specify data directory if needed
fn_clinical_data = "data/ALD_study/processed/ald_metadata_cli.csv"
fn_qc_samples = ''  # 'data/ALD_study/processed/qc_plasma_proteinGroups.pkl'
f_annotations = 'data/ALD_study/processed/ald_plasma_proteinGroups_id_mappings.csv'


target: str = 'kleiner'
covar: str = 'age,bmi,gender_num,nas_steatosis_ordinal,abstinent_num'

file_format = "csv"
model_key = 'VAE'  # model(s) to evaluate
model = None  # default same as model_key, but could be overwritten (edge case)
value_name = 'intensity'
out_folder = 'diff_analysis'
template_pred = 'pred_real_na_{}.csv'  # fixed, do not change

# Parameters
f_annotations = None
folder_experiment = "runs/alzheimer_study"
fn_clinical_data = "runs/alzheimer_study/data/clinical_data.csv"
target = "AD"
covar = "age,Kiel,Magdeburg,Sweden"
model_key = "CF"
out_folder = "diff_analysis"

Add set parameters to configuration

Hide code cell source

 
if not model:
    model = model_key
params = pimmslearn.nb.get_params(args, globals=globals(), remove=True)
params

root - INFO     Removed from global namespace: folder_experiment
root - INFO     Removed from global namespace: folder_data
root - INFO     Removed from global namespace: fn_clinical_data
root - INFO     Removed from global namespace: fn_qc_samples
root - INFO     Removed from global namespace: f_annotations
root - INFO     Removed from global namespace: target
root - INFO     Removed from global namespace: covar
root - INFO     Removed from global namespace: file_format
root - INFO     Removed from global namespace: model_key
root - INFO     Removed from global namespace: model
root - INFO     Removed from global namespace: value_name
root - INFO     Removed from global namespace: out_folder
root - INFO     Removed from global namespace: template_pred

{'folder_experiment': 'runs/alzheimer_study',
 'folder_data': '',
 'fn_clinical_data': 'runs/alzheimer_study/data/clinical_data.csv',
 'fn_qc_samples': '',
 'f_annotations': None,
 'target': 'AD',
 'covar': 'age,Kiel,Magdeburg,Sweden',
 'file_format': 'csv',
 'model_key': 'CF',
 'model': 'CF',
 'value_name': 'intensity',
 'out_folder': 'diff_analysis',
 'template_pred': 'pred_real_na_{}.csv'}

Hide code cell source

 
args = pimmslearn.nb.Config()
args.fn_clinical_data = Path(params["fn_clinical_data"])
args.folder_experiment = Path(params["folder_experiment"])
args = pimmslearn.nb.add_default_paths(args,
                                 out_root=(args.folder_experiment
                                           / params["out_folder"]
                                           / params["target"]
                                           ))
args.covar = params["covar"].split(',')
args.update_from_dict(params)
args

root - INFO     Already set attribute: folder_experiment has value runs/alzheimer_study
root - INFO     Already set attribute: fn_clinical_data has value runs/alzheimer_study/data/clinical_data.csv
root - INFO     Already set attribute: covar has value age,Kiel,Magdeburg,Sweden
root - INFO     Already set attribute: out_folder has value diff_analysis

{'covar': ['age', 'Kiel', 'Magdeburg', 'Sweden'],
 'data': PosixPath('runs/alzheimer_study/data'),
 'f_annotations': None,
 'file_format': 'csv',
 'fn_clinical_data': PosixPath('runs/alzheimer_study/data/clinical_data.csv'),
 'fn_qc_samples': '',
 'folder_data': '',
 'folder_experiment': PosixPath('runs/alzheimer_study'),
 'model': 'CF',
 'model_key': 'CF',
 'out_figures': PosixPath('runs/alzheimer_study/figures'),
 'out_folder': PosixPath('runs/alzheimer_study/diff_analysis/AD'),
 'out_metrics': PosixPath('runs/alzheimer_study'),
 'out_models': PosixPath('runs/alzheimer_study'),
 'out_preds': PosixPath('runs/alzheimer_study/preds'),
 'target': 'AD',
 'template_pred': 'pred_real_na_{}.csv',
 'value_name': 'intensity'}

Outputs of this notebook will be stored here:

Hide code cell source

 
files_out = {}
args.out_folder

PosixPath('runs/alzheimer_study/diff_analysis/AD')

Data#

MS proteomics or specified omics data#

Aggregated from data splits of the imputation workflow run before.

Hide code cell source

 
data = pimmslearn.io.datasplits.DataSplits.from_folder(
    args.data, file_format=args.file_format)

pimmslearn.io.datasplits - INFO     Loaded 'train_X' from file: runs/alzheimer_study/data/train_X.csv
pimmslearn.io.datasplits - INFO     Loaded 'val_y' from file: runs/alzheimer_study/data/val_y.csv
pimmslearn.io.datasplits - INFO     Loaded 'test_y' from file: runs/alzheimer_study/data/test_y.csv

Hide code cell source

 
observed = pd.concat([data.train_X, data.val_y, data.test_y])
observed

Sample ID   protein groups                                                                
Sample_000  A0A024QZX5;A0A087X1N8;P35237                                                     15.912
            A0A024R0T9;K7ER74;P02655                                                         16.852
            A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8   15.570
            A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503                                          16.481
            A0A075B6H7                                                                       17.301
                                                                                              ...  
Sample_209  Q96ID5                                                                           16.074
            Q9H492;Q9H492-2                                                                  13.173
            Q9HC57                                                                           14.207
            Q9NPH3;Q9NPH3-2;Q9NPH3-5                                                         14.962
            Q9UGM5;Q9UGM5-2                                                                  16.871
Name: intensity, Length: 252009, dtype: float64

Clinical data#

Describe numerical data specified for use:

Hide code cell source

 
df_clinic = pd.read_csv(args.fn_clinical_data, index_col=0)
df_clinic = df_clinic.loc[observed.index.levels[0]]
cols_clinic = pimmslearn.pandas.get_columns_accessor(df_clinic)
df_clinic[[args.target, *args.covar]].describe()
AD age Kiel Magdeburg Sweden
count 210.000 197.000 210.000 210.000 210.000
mean 0.419 67.726 0.076 0.181 0.286
std 0.495 12.123 0.266 0.386 0.453
min 0.000 20.000 0.000 0.000 0.000
25% 0.000 63.000 0.000 0.000 0.000
50% 0.000 70.000 0.000 0.000 0.000
75% 1.000 74.000 0.000 0.000 1.000
max 1.000 88.000 1.000 1.000 1.000

Hide code cell source

 
# ## Additional annotations
# - additional annotations of features (e.g. gene names for protein groups)

feat_name = observed.index.names[-1]
if args.f_annotations:
    gene_to_PG = pd.read_csv(args.f_annotations)
    gene_to_PG = gene_to_PG.drop_duplicates().set_index(feat_name)
    fname = args.out_folder / Path(args.f_annotations).name
    gene_to_PG.to_csv(fname)
    files_out[fname.name] = fname.as_posix()
else:
    gene_to_PG = None
gene_to_PG

Entries with missing values

  • see how many rows have one missing values (for target and covariates)

  • only complete data is used for Differential Analysis

  • covariates are not imputed

Hide code cell source

 
df_clinic[[args.target, *args.covar]].isna().any(axis=1).sum()

np.int64(13)

Data description of data used:

Hide code cell source

 
mask_sample_with_complete_clinical_data = df_clinic[[args.target, *args.covar]].notna().all(axis=1)
fname = args.out_folder / 'mask_sample_with_complete_clinical_data.csv'
files_out[fname.name] = fname.as_posix()
mask_sample_with_complete_clinical_data.to_csv(fname)

idx_complete_data = (mask_sample_with_complete_clinical_data
                     .loc[mask_sample_with_complete_clinical_data]
                     .index)
df_clinic.loc[idx_complete_data, [args.target, *args.covar]].describe()
AD age Kiel Magdeburg Sweden
count 197.000 197.000 197.000 197.000 197.000
mean 0.447 67.726 0.081 0.193 0.305
std 0.498 12.123 0.274 0.396 0.461
min 0.000 20.000 0.000 0.000 0.000
25% 0.000 63.000 0.000 0.000 0.000
50% 0.000 70.000 0.000 0.000 0.000
75% 1.000 74.000 0.000 0.000 1.000
max 1.000 88.000 1.000 1.000 1.000

Hide code cell source

 
df_clinic.loc[idx_complete_data, args.target].value_counts()

AD
0   109
1    88
Name: count, dtype: int64

Check which patients with kleiner score have misssing covariates:

Hide code cell source

 
df_clinic.loc[(~mask_sample_with_complete_clinical_data
               & df_clinic[args.target].notna()),
              [args.target, *args.covar]]
AD age Kiel Magdeburg Sweden
Sample ID
Sample_021 0 NaN 0 0 0
Sample_065 0 NaN 0 0 0
Sample_066 0 NaN 0 0 0
Sample_067 0 NaN 0 0 0
Sample_082 0 NaN 0 0 0
Sample_108 0 NaN 0 0 0
Sample_120 0 NaN 0 0 0
Sample_135 0 NaN 0 0 0
Sample_138 0 NaN 0 0 0
Sample_145 0 NaN 0 0 0
Sample_147 0 NaN 0 0 0
Sample_181 0 NaN 0 0 0
Sample_204 0 NaN 0 0 0

Save feature frequency of observed data based on complete clinical data

Hide code cell source

 
feat_freq_observed = observed.unstack().loc[idx_complete_data].notna().sum()
feat_freq_observed.name = 'frequency'

fname = args.folder_experiment / 'freq_features_observed.csv'
files_out['feat_freq_observed'] = fname.as_posix()
logger.info(fname)
feat_freq_observed.to_csv(fname)
ax = feat_freq_observed.sort_values().plot(marker='.', rot=90)
_ = ax.set_xticklabels([l_.get_text().split(';')[0] for l_ in ax.get_xticklabels()])

root - INFO     runs/alzheimer_study/freq_features_observed.csv
../../../_images/fb002abe7ec85957a9eace7cfec09507fc4b59ad59e7898a2e6e6b2afb71bd28.png

ALD study approach using all measurements#

Use parameters as specified in ALD study.

Hide code cell source

 
DATA_COMPLETENESS = 0.6
# MIN_N_PROTEIN_GROUPS: int = 200
FRAC_PROTEIN_GROUPS: int = 0.622
CV_QC_SAMPLE: float = 0.4  # Coef. of variation on 13 QC samples

ald_study, cutoffs = pimmslearn.analyzers.diff_analysis.select_raw_data(observed.unstack(
), data_completeness=DATA_COMPLETENESS, frac_protein_groups=FRAC_PROTEIN_GROUPS)

ald_study

root - INFO     Initally: N samples: 210, M feat: 1421
root - INFO     Dropped features quantified in less than 126 samples.
root - INFO     After feat selection: N samples: 210, M feat: 1213
root - INFO     Min No. of Protein-Groups in single sample: 754
root - INFO     Finally: N samples: 210, M feat: 1213
protein groups A0A024QZX5;A0A087X1N8;P35237 A0A024R0T9;K7ER74;P02655 A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8 A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503 A0A075B6H9 A0A075B6I0 A0A075B6I1 A0A075B6I6 A0A075B6I9 A0A075B6J9 ... Q9Y653;Q9Y653-2;Q9Y653-3 Q9Y696 Q9Y6C2 Q9Y6N6 Q9Y6N7;Q9Y6N7-2;Q9Y6N7-4 Q9Y6R7 Q9Y6X5 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y9 S4R3U6
Sample ID
Sample_000 15.912 16.852 15.570 16.481 20.246 16.764 17.584 16.988 20.054 NaN ... 16.012 15.178 NaN 15.050 16.842 19.863 NaN 19.563 12.837 12.805
Sample_001 15.936 16.874 15.519 16.387 19.941 18.786 17.144 NaN 19.067 16.188 ... 15.528 15.576 NaN 14.833 16.597 20.299 15.556 19.386 13.970 12.442
Sample_002 16.111 14.523 15.935 16.416 19.251 16.832 15.671 17.012 18.569 NaN ... 15.229 14.728 13.757 15.118 17.440 19.598 15.735 20.447 12.636 12.505
Sample_003 16.107 17.032 15.802 16.979 19.628 17.852 18.877 14.182 18.985 13.438 ... 15.495 14.590 14.682 15.140 17.356 19.429 NaN 20.216 12.627 12.445
Sample_004 15.603 15.331 15.375 16.679 20.450 18.682 17.081 14.140 19.686 14.495 ... 14.757 15.094 14.048 15.256 17.075 19.582 15.328 19.867 13.145 12.235
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Sample_205 15.682 16.886 14.910 16.482 17.705 17.039 NaN 16.413 19.102 16.064 ... 15.235 15.684 14.236 15.415 17.551 17.922 16.340 19.928 12.929 11.802
Sample_206 15.798 17.554 15.600 15.938 18.154 18.152 16.503 16.860 18.538 15.288 ... 15.422 16.106 NaN 15.345 17.084 18.708 14.249 19.433 NaN NaN
Sample_207 15.739 16.877 15.469 16.898 18.636 17.950 16.321 16.401 18.849 17.580 ... 15.808 16.098 14.403 15.715 16.586 18.725 16.138 19.599 13.637 11.174
Sample_208 15.477 16.779 14.995 16.132 14.908 17.530 NaN 16.119 18.368 15.202 ... 15.157 16.712 NaN 14.640 16.533 19.411 15.807 19.545 13.216 NaN
Sample_209 15.727 17.261 15.175 16.235 17.893 17.744 16.371 15.780 18.806 16.532 ... 15.237 15.652 15.211 14.205 16.749 19.275 15.732 19.577 11.042 11.791

210 rows × 1213 columns

Hide code cell source

 
if args.fn_qc_samples:
    # Move this to data-preprocessing
    qc_samples = pd.read_pickle(args.fn_qc_samples)
    qc_cv_feat = qc_samples.std() / qc_samples.mean()
    qc_cv_feat = qc_cv_feat.rename(qc_samples.columns.name)
    fig, ax = plt.subplots(figsize=(4, 7))
    ax = qc_cv_feat.plot.box(ax=ax)
    ax.set_ylabel('Coefficient of Variation')
    pimmslearn.savefig(fig, name='cv_qc_samples', folder=args.out_figures)
    print((qc_cv_feat < CV_QC_SAMPLE).value_counts())
    # only to ald_study data
    ald_study = ald_study[pimmslearn.analyzers.diff_analysis.select_feat(qc_samples[ald_study.columns])]

ald_study
protein groups A0A024QZX5;A0A087X1N8;P35237 A0A024R0T9;K7ER74;P02655 A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8 A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503 A0A075B6H9 A0A075B6I0 A0A075B6I1 A0A075B6I6 A0A075B6I9 A0A075B6J9 ... Q9Y653;Q9Y653-2;Q9Y653-3 Q9Y696 Q9Y6C2 Q9Y6N6 Q9Y6N7;Q9Y6N7-2;Q9Y6N7-4 Q9Y6R7 Q9Y6X5 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y9 S4R3U6
Sample ID
Sample_000 15.912 16.852 15.570 16.481 20.246 16.764 17.584 16.988 20.054 NaN ... 16.012 15.178 NaN 15.050 16.842 19.863 NaN 19.563 12.837 12.805
Sample_001 15.936 16.874 15.519 16.387 19.941 18.786 17.144 NaN 19.067 16.188 ... 15.528 15.576 NaN 14.833 16.597 20.299 15.556 19.386 13.970 12.442
Sample_002 16.111 14.523 15.935 16.416 19.251 16.832 15.671 17.012 18.569 NaN ... 15.229 14.728 13.757 15.118 17.440 19.598 15.735 20.447 12.636 12.505
Sample_003 16.107 17.032 15.802 16.979 19.628 17.852 18.877 14.182 18.985 13.438 ... 15.495 14.590 14.682 15.140 17.356 19.429 NaN 20.216 12.627 12.445
Sample_004 15.603 15.331 15.375 16.679 20.450 18.682 17.081 14.140 19.686 14.495 ... 14.757 15.094 14.048 15.256 17.075 19.582 15.328 19.867 13.145 12.235
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Sample_205 15.682 16.886 14.910 16.482 17.705 17.039 NaN 16.413 19.102 16.064 ... 15.235 15.684 14.236 15.415 17.551 17.922 16.340 19.928 12.929 11.802
Sample_206 15.798 17.554 15.600 15.938 18.154 18.152 16.503 16.860 18.538 15.288 ... 15.422 16.106 NaN 15.345 17.084 18.708 14.249 19.433 NaN NaN
Sample_207 15.739 16.877 15.469 16.898 18.636 17.950 16.321 16.401 18.849 17.580 ... 15.808 16.098 14.403 15.715 16.586 18.725 16.138 19.599 13.637 11.174
Sample_208 15.477 16.779 14.995 16.132 14.908 17.530 NaN 16.119 18.368 15.202 ... 15.157 16.712 NaN 14.640 16.533 19.411 15.807 19.545 13.216 NaN
Sample_209 15.727 17.261 15.175 16.235 17.893 17.744 16.371 15.780 18.806 16.532 ... 15.237 15.652 15.211 14.205 16.749 19.275 15.732 19.577 11.042 11.791

210 rows × 1213 columns

Hide code cell source

 
fig, axes = pimmslearn.plotting.plot_cutoffs(observed.unstack(),
                                       feat_completness_over_samples=cutoffs.feat_completness_over_samples,
                                       min_feat_in_sample=cutoffs.min_feat_in_sample)
pimmslearn.savefig(fig, name='tresholds_normal_imputation', folder=args.out_figures)

pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/figures/tresholds_normal_imputation
../../../_images/82e5dfe13ea67779ac6223852204ac7eb9489c50c34ffa70e96393281adf1e84.png

Load model predictions for (real) missing data#

Load from:

Hide code cell source

 
# available_files = list(args.out_preds.iterdir())
template_pred = str(args.out_preds / args.template_pred)
fname = args.out_preds / args.template_pred.format(args.model)
fname

PosixPath('runs/alzheimer_study/preds/pred_real_na_CF.csv')

Baseline comparison:

  • in case of RSN -> use filtering as done in original ALD study (Niu et al. 2022)

  • otherwise -> use all data

Use columns which are provided by model

Hide code cell source

 
pred_real_na = None
if args.model_key and str(args.model_key) != 'None':
    pred_real_na = (pimmslearn
                    .analyzers
                    .compare_predictions
                    .load_single_csv_pred_file(fname)
                    )
else:
    logger.info('No model key provided -> no imputation of data.')

if args.model_key == 'RSN':
    logger.info('Filtering of data as done in original paper for RSN.')
    # Select only idx from RSN which are selected by ald study cutoffs
    idx_to_sel = ald_study.columns.intersection(pred_real_na.index.levels[-1])
    pred_real_na = pred_real_na.loc[pd.IndexSlice[:, idx_to_sel]]
pred_real_na

Sample ID   protein groups          
Sample_000  A0A075B6J9                 15.273
            A0A075B6Q5                 15.901
            A0A075B6R2                 16.536
            A0A075B6S5                 16.008
            A0A087WSY4                 16.309
                                        ...  
Sample_209  Q9P1W8;Q9P1W8-2;Q9P1W8-4   16.468
            Q9UI40;Q9UI40-2            16.196
            Q9UIW2                     16.985
            Q9UMX0;Q9UMX0-2;Q9UMX0-4   13.503
            Q9UP79                     16.189
Name: intensity, Length: 46401, dtype: float64

Plot unchanged observed intensities to imputed intensity distribution (if available):

Hide code cell source

 
def plot_distributions(observed: pd.Series,
                       imputation: pd.Series = None,
                       model_key: str = 'MODEL',
                       figsize=(4, 3),
                       sharex=True):
    """Plots distributions of intensities provided as dictionary of labels to pd.Series."""
    series_ = [observed, imputation] if imputation is not None else [observed]
    min_bin, max_bin = pimmslearn.plotting.data.get_min_max_iterable([observed])

    if imputation is not None:
        fig, axes = plt.subplots(len(series_), figsize=figsize, sharex=sharex)
        ax = axes[0]
    else:
        fig, ax = plt.subplots(1, figsize=figsize, sharex=sharex)

    bins = range(min_bin, max_bin + 1, 1)

    label = 'observed measurments'
    ax = observed.hist(ax=ax, bins=bins, color='grey')
    ax.set_title(f'{label} (N={len(observed):,d})')
    ax.set_ylabel('observations')
    ax.locator_params(axis='y', integer=True)
    ax.yaxis.set_major_formatter("{x:,.0f}")

    if imputation is not None:
        ax = axes[1]
        label = f'Missing values imputed using {model_key.upper()}'
        color = pimmslearn.plotting.defaults.color_model_mapping.get(model_key, None)
        if color is None:
            color = f'C{1}'
        ax = imputation.hist(ax=ax, bins=bins, color=color)
        ax.set_title(f'{label} (N={len(imputation):,d})')
        ax.set_ylabel('observations')
        ax.locator_params(axis='y', integer=True)
        ax.yaxis.set_major_formatter("{x:,.0f}")
    return fig, bins


pimmslearn.plotting.make_large_descriptors(6)
fig, bins = plot_distributions(observed,
                               imputation=pred_real_na,
                               model_key=args.model_key, figsize=(2.5, 2))
fname = args.out_folder / 'dist_plots' / f'real_na_obs_vs_{args.model_key}.pdf'
files_out[fname.name] = fname.as_posix()
pimmslearn.savefig(fig, name=fname)

pimmslearn.plotting - INFO     Saved Figures to runs/alzheimer_study/diff_analysis/AD/dist_plots/real_na_obs_vs_CF.pdf
../../../_images/74332e688ffdd3e8b63df1fd98b73eac4e62365e25b85a6322e15f2bccd39699.png

Dump frequency of histograms to file for reporting (if imputed values are used)

Hide code cell source

 
if pred_real_na is not None:
    counts_per_bin = pd.concat([
        pimmslearn.pandas.get_counts_per_bin(observed.to_frame('observed'), bins=bins),
        pimmslearn.pandas.get_counts_per_bin(pred_real_na.to_frame(args.model_key), bins=bins)
    ], axis=1)
    counts_per_bin.to_excel(fname.with_suffix('.xlsx'))
    logger.info("Counts per bin saved to %s", fname.with_suffix('.xlsx'))
    display(counts_per_bin)

/home/runner/work/pimms/pimms/project/.snakemake/conda/924ec7e362d761ecf0807b9074d79999_/lib/python3.12/site-packages/pimmslearn/pandas/__init__.py:320: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  _series = (pd.cut(df[col], bins=bins).to_frame().groupby(col).size())
/home/runner/work/pimms/pimms/project/.snakemake/conda/924ec7e362d761ecf0807b9074d79999_/lib/python3.12/site-packages/pimmslearn/pandas/__init__.py:320: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
  _series = (pd.cut(df[col], bins=bins).to_frame().groupby(col).size())
root - INFO     Counts per bin saved to runs/alzheimer_study/diff_analysis/AD/dist_plots/real_na_obs_vs_CF.xlsx
observed CF
bin
(6, 7] 1 0
(7, 8] 4 0
(8, 9] 39 0
(9, 10] 136 12
(10, 11] 529 443
(11, 12] 1,731 1,744
(12, 13] 4,644 4,062
(13, 14] 12,161 7,523
(14, 15] 27,515 11,931
(15, 16] 44,723 11,601
(16, 17] 45,981 5,956
(17, 18] 36,274 1,801
(18, 19] 25,049 634
(19, 20] 20,386 318
(20, 21] 13,495 240
(21, 22] 8,234 102
(22, 23] 4,885 20
(23, 24] 2,459 10
(24, 25] 1,237 3
(25, 26] 1,392 0
(26, 27] 643 0
(27, 28] 88 1
(28, 29] 216 0
(29, 30] 163 0

Mean shift by model#

Compare how imputed values are shifted in comparsion to overall distribution.

First by using all intensities without any grouping:

Hide code cell source

 
if pred_real_na is not None:
    shifts = (pimmslearn.imputation.compute_moments_shift(observed, pred_real_na,
                                                    names=('observed', args.model_key)))
    display(pd.DataFrame(shifts).T)
mean std mean shift (in std) std shrinkage
observed 17.119 2.567 NaN NaN
CF 14.775 1.643 0.914 0.640

Then by averaging over the calculation by sample:

Hide code cell source

 
if pred_real_na is not None:
    index_level = 0  # per sample
    mean_by_sample = pd.DataFrame(
        {'observed': pimmslearn.imputation.stats_by_level(observed, index_level=index_level),
         args.model_key: pimmslearn.imputation.stats_by_level(pred_real_na, index_level=index_level)
         })
    mean_by_sample.loc['mean_shift'] = (mean_by_sample.loc['mean', 'observed'] -
                                        mean_by_sample.loc['mean']).abs() / mean_by_sample.loc['std', 'observed']
    mean_by_sample.loc['std shrinkage'] = mean_by_sample.loc['std'] / \
        mean_by_sample.loc['std', 'observed']
    display(mean_by_sample)
observed CF
count 1,200.043 220.957
mean 17.133 14.748
std 2.564 1.596
mean_shift 0.000 0.930
std shrinkage 1.000 0.623

Differential analysis#

Combine observed and imputed data (if available) for differential analysis:

Hide code cell source

 
df = pd.concat([observed, pred_real_na]).unstack()
df.loc[idx_complete_data]
protein groups A0A024QZX5;A0A087X1N8;P35237 A0A024R0T9;K7ER74;P02655 A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8 A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503 A0A075B6H7 A0A075B6H9 A0A075B6I0 A0A075B6I1 A0A075B6I6 A0A075B6I9 ... Q9Y653;Q9Y653-2;Q9Y653-3 Q9Y696 Q9Y6C2 Q9Y6N6 Q9Y6N7;Q9Y6N7-2;Q9Y6N7-4 Q9Y6R7 Q9Y6X5 Q9Y6Y8;Q9Y6Y8-2 Q9Y6Y9 S4R3U6
Sample ID
Sample_000 15.912 16.852 15.570 16.481 17.301 20.246 16.764 17.584 16.988 20.054 ... 16.012 15.178 14.642 15.050 16.842 19.863 15.796 19.563 12.837 12.805
Sample_001 15.936 16.874 15.519 16.387 13.796 19.941 18.786 17.144 16.525 19.067 ... 15.528 15.576 14.423 14.833 16.597 20.299 15.556 19.386 13.970 12.442
Sample_002 16.111 14.523 15.935 16.416 18.175 19.251 16.832 15.671 17.012 18.569 ... 15.229 14.728 13.757 15.118 17.440 19.598 15.735 20.447 12.636 12.505
Sample_003 16.107 17.032 15.802 16.979 15.963 19.628 17.852 18.877 14.182 18.985 ... 15.495 14.590 14.682 15.140 17.356 19.429 15.684 20.216 12.627 12.445
Sample_004 15.603 15.331 15.375 16.679 15.473 20.450 18.682 17.081 14.140 19.686 ... 14.757 15.094 14.048 15.256 17.075 19.582 15.328 19.867 13.145 12.235
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
Sample_205 15.682 16.886 14.910 16.482 14.920 17.705 17.039 15.316 16.413 19.102 ... 15.235 15.684 14.236 15.415 17.551 17.922 16.340 19.928 12.929 11.802
Sample_206 15.798 17.554 15.600 15.938 15.671 18.154 18.152 16.503 16.860 18.538 ... 15.422 16.106 15.108 15.345 17.084 18.708 14.249 19.433 12.006 11.538
Sample_207 15.739 16.877 15.469 16.898 15.068 18.636 17.950 16.321 16.401 18.849 ... 15.808 16.098 14.403 15.715 16.586 18.725 16.138 19.599 13.637 11.174
Sample_208 15.477 16.779 14.995 16.132 14.228 14.908 17.530 15.649 16.119 18.368 ... 15.157 16.712 14.292 14.640 16.533 19.411 15.807 19.545 13.216 11.486
Sample_209 15.727 17.261 15.175 16.235 14.859 17.893 17.744 16.371 15.780 18.806 ... 15.237 15.652 15.211 14.205 16.749 19.275 15.732 19.577 11.042 11.791

197 rows × 1421 columns

Hide code cell source

 
# * if some features were not imputed -> drop them
# ? could be changed: let a model decide if a feature should be imputed, otherwise don't.
if pred_real_na is not None:
    if df.isna().sum().sum():
        logger.warning("DataFrame has missing entries after imputation.")
        logger.info("Drop columns with missing values.")
    df = df.dropna(axis=1)

Results for target and clinical variables:

Hide code cell source

 
scores = njab.stats.ancova.AncovaAll(df_proteomics=df,
                                     df_clinic=df_clinic,
                                     target=args.target,
                                     covar=args.covar,
                                     value_name=args.value_name
                                     ).ancova()
# features are in first index position
feat_idx = scores.index.get_level_values(0)
if gene_to_PG is not None:
    scores = (scores
              .join(gene_to_PG)
              .set_index(gene_to_PG.columns.to_list(), append=True)
              )
scores
SS DF F p-unc np2 -Log10 pvalue qvalue rejected
protein groups Source
A0A024QZX5;A0A087X1N8;P35237 AD 1.046 1 7.580 0.006 0.038 2.189 0.019 True
age 0.002 1 0.015 0.903 0.000 0.044 0.937 False
Kiel 0.237 1 1.714 0.192 0.009 0.717 0.308 False
Magdeburg 0.457 1 3.311 0.070 0.017 1.152 0.139 False
Sweden 1.703 1 12.341 0.001 0.061 3.257 0.002 True
... ... ... ... ... ... ... ... ... ...
S4R3U6 AD 1.235 1 2.661 0.104 0.014 0.981 0.190 False
age 0.929 1 2.002 0.159 0.010 0.799 0.265 False
Kiel 1.513 1 3.260 0.073 0.017 1.139 0.142 False
Magdeburg 1.112 1 2.396 0.123 0.012 0.909 0.217 False
Sweden 15.111 1 32.552 0.000 0.146 7.360 0.000 True

7105 rows × 8 columns

Only for target:

Hide code cell source

 
scores.columns = pd.MultiIndex.from_product([[str(args.model_key)], scores.columns],
                                            names=('model', 'var'))
scores.loc[pd.IndexSlice[:, args.target], :]
model CF
var SS DF F p-unc np2 -Log10 pvalue qvalue rejected
protein groups Source
A0A024QZX5;A0A087X1N8;P35237 AD 1.046 1 7.580 0.006 0.038 2.189 0.019 True
A0A024R0T9;K7ER74;P02655 AD 2.814 1 4.574 0.034 0.023 1.472 0.076 False
A0A024R3W6;A0A024R412;O60462;O60462-2;O60462-3;O60462-4;O60462-5;Q7LBX6;X5D2Q8 AD 0.119 1 0.948 0.331 0.005 0.480 0.467 False
A0A024R644;A0A0A0MRU5;A0A1B0GWI2;O75503 AD 0.179 1 1.291 0.257 0.007 0.590 0.385 False
A0A075B6H7 AD 8.095 1 10.827 0.001 0.054 2.924 0.004 True
... ... ... ... ... ... ... ... ... ...
Q9Y6R7 AD 0.675 1 1.850 0.175 0.010 0.756 0.286 False
Q9Y6X5 AD 0.685 1 2.032 0.156 0.011 0.808 0.261 False
Q9Y6Y8;Q9Y6Y8-2 AD 0.973 1 3.028 0.083 0.016 1.079 0.159 False
Q9Y6Y9 AD 0.333 1 0.517 0.473 0.003 0.325 0.600 False
S4R3U6 AD 1.235 1 2.661 0.104 0.014 0.981 0.190 False

1421 rows × 8 columns

Save all results to file:

Hide code cell source

 
fname = args.out_folder / 'scores' / f'diff_analysis_scores_{str(args.model_key)}.pkl'
files_out[fname.name] = fname.as_posix()
fname.parent.mkdir(exist_ok=True, parents=True)
scores.to_pickle(fname)
fname

PosixPath('runs/alzheimer_study/diff_analysis/AD/scores/diff_analysis_scores_CF.pkl')

Saved files:

Hide code cell source

 
files_out

{'mask_sample_with_complete_clinical_data.csv': 'runs/alzheimer_study/diff_analysis/AD/mask_sample_with_complete_clinical_data.csv',
 'feat_freq_observed': 'runs/alzheimer_study/freq_features_observed.csv',
 'real_na_obs_vs_CF.pdf': 'runs/alzheimer_study/diff_analysis/AD/dist_plots/real_na_obs_vs_CF.pdf',
 'diff_analysis_scores_CF.pkl': 'runs/alzheimer_study/diff_analysis/AD/scores/diff_analysis_scores_CF.pkl'}
Contents