"""
Placeholder implementations for functions that need to be implemented.
"""
from typing import List, Tuple, Dict, Any, Optional, Union, Sequence, Callable
import pandas as pd
import numpy as np
from numpy.typing import ArrayLike
def summarize_reps_no_filtering(
data: pd.DataFrame,
col4val: str,
col4anno: str,
) -> pd.DataFrame:
"""
Summarize replicates without filtering.
Args:
data: DataFrame containing at least columns for annotation (col4anno),
SpotType, and intensity column (col4val).
col4val: name of the intensity column to fetch when index_or_int="Intensities".
col4anno: name of the annotation column grouping replicates.
Returns:
replicate_matrix: 2D numpy array of shape (n_items, max_replicates), filled with
indices or values, using np.nan where missing.
index_pos_controls: list of row indices in replicate_matrix corresponding to positive controls.
index_neg_controls: list of row indices in replicate_matrix corresponding to negative controls.
"""
raise NotImplementedError
[docs]
def generate_replicate_matrix(
data: pd.DataFrame,
min_reps: int,
col: str,
anno: str,
) -> Tuple[np.ndarray, List[int], List[int]]:
"""
Generate a replicate matrix from the given data.
Args:
data: DataFrame containing at least columns [col4val, col4anno].
min_reps: Minimum number of replicates required to keep an ID.
col: name of the intensity column to fetch when index_or_int="Intensities".
anno: name of the annotation column grouping replicates.
Returns:
replicate_matrix: 2D numpy array of shape (n_items, max_replicates), filled with
indices or values, using np.nan where missing.
index_pos_controls: list of row indices in replicate_matrix corresponding to positive controls.
index_neg_controls: list of row indices in replicate_matrix corresponding to negative controls.
"""
raise NotImplementedError
[docs]
def summarize_reps_no_filtering(
data: pd.DataFrame,
col4val: str,
col4anno: str,
) -> pd.DataFrame:
"""
Summarize replicates without filtering.
Args:
data: DataFrame containing at least columns [col4val, col4anno].
col4val: name of the intensity column to fetch when index_or_int="Intensities".
col4anno: name of the annotation column grouping replicates.
Returns:
DataFrame with col4val
"""
raise NotImplementedError
[docs]
def PdfPages(
output_file: str
) :
raise NotImplementedError