pg-sui 1.0.2.1__py3-none-any.whl → 1.6.8__py3-none-any.whl

pgsui/impute/deterministic/imputers/nmf.py

@@ -0,0 +1,221 @@
+from pathlib import Path
+from typing import Dict, List
+
+# Third-party imports
+import numpy as np
+import pandas as pd
+
+
+class ImputeNMF:
+    """Impute missing data using matrix factorization. If ``by_populations=False`` then imputation is by global allele frequency. If ``by_populations=True`` then imputation is by population-wise allele frequency.
+
+    Args:
+        genotype_data (GenotypeData object or None, optional): GenotypeData instance.
+        latent_features (float, optional): The number of latent variables used to reduce dimensionality of the data. Defaults to 2.
+        learning_rate (float, optional): The learning rate for the optimizers. Adjust if the loss is learning too slowly. Defaults to 0.1.
+        tol (float, optional): Tolerance of the stopping condition. Defaults to 1e-3.
+        missing (int, optional): Missing data value. Defaults to -9.
+        prefix (str, optional): Prefix for writing output files. Defaults to "output".
+        verbose (bool, optional): Whether to print status updates. Set to False for no status updates. Defaults to True.
+        **kwargs (Dict[str, bool | List[List[int]] | None | float | int | str]): Additional keyword arguments to supply. Primarily for internal purposes. Options include: {"iterative_mode": bool, "validation_mode": bool, "gt": List[List[int]]}. "iterative_mode" determines whether ``ImputeAlleleFreq`` is being used as the initial imputer in ``IterativeImputer``. "gt" is used internally for the simple imputers during grid searches and validation. If ``genotype_data is None`` then ``gt`` cannot also be None, and vice versa. Only one of ``gt`` or ``genotype_data`` can be set.
+
+    Attributes:
+        imputed (GenotypeData): New GenotypeData instance with imputed data.
+
+    Example:
+        >>>data = GenotypeData(
+        >>>    filename="test.str",
+        >>>    filetype="structure",
+        >>>    popmapfile="test.popmap",
+        >>>)
+        >>>
+        >>>nmf = ImputeMF(
+        >>>    genotype_data=data,
+        >>>    by_populations=True,
+        >>>)
+        >>>
+        >>> # Get GenotypeData instance.
+        >>>gd_nmf = nmf.imputed
+
+    Raises:
+        TypeError: genotype_data cannot be NoneType.
+    """
+
+    def __init__(
+        self,
+        genotype_data,
+        *,
+        latent_features: int = 2,
+        max_iter: int = 100,
+        learning_rate: float = 0.0002,
+        regularization_param: float = 0.02,
+        tol: float = 0.1,
+        n_fail: int = 20,
+        missing: int = -9,
+        prefix: str = "imputer",
+        verbose: bool = True,
+        **kwargs: Dict[str, bool | List[List[int]] | None | float | int | str],
+    ) -> None:
+        self.max_iter = max_iter
+        self.latent_features = latent_features
+        self.n_fail = n_fail
+        self.learning_rate = learning_rate
+        self.tol = tol
+        self.regularization_param = regularization_param
+        self.missing = missing
+        self.prefix = prefix
+        self.verbose = verbose
+        self.iterative_mode = kwargs.get("iterative_mode", False)
+        self.validation_mode = kwargs.get("validation_mode", False)
+
+        gt = kwargs.get("gt", None)
+
+        if genotype_data is None and gt is None:
+            raise TypeError("GenotypeData and gt cannot both be NoneType.")
+
+        if gt is None:
+            X = genotype_data.genotypes_012(fmt="numpy")
+        else:
+            X = gt.copy()
+        imputed012 = pd.DataFrame(self.fit_predict(X))
+        genotype_data = genotype_data.copy()
+        genotype_data.snp_data = genotype_data.decode_012(
+            imputed012, prefix=prefix, write_output=False
+        )
+
+        if self.validation_mode:
+            self.imputed = imputed012.to_numpy()
+        else:
+            self.imputed = genotype_data
+
+    @property
+    def genotypes_012(self):
+        return self.imputed.genotypes012
+
+    @property
+    def snp_data(self):
+        return self.imputed.snp_data
+
+    @property
+    def alignment(self):
+        return self.imputed.alignment
+
+    def fit_predict(self, X):
+        # imputation
+        if self.verbose:
+            print(f"Doing MF imputation...")
+        R = X
+        R = R.astype(int)
+        R[R == self.missing] = -9
+        R = R + 1
+        R[R < 0] = 0
+        n_row = len(R)
+        n_col = len(R[0])
+        p = np.random.rand(n_row, self.latent_features)
+        q = np.random.rand(n_col, self.latent_features)
+        q_t = q.T
+        fails = 0
+        e_current = None
+        for step in range(self.max_iter):
+            for i in range(n_row):
+                for j in range(n_col):
+                    if R[i][j] > 0:
+                        eij = R[i][j] - np.dot(p[i, :], q_t[:, j])
+                        for k in range(self.latent_features):
+                            p[i][k] = p[i][k] + self.learning_rate * (
+                                2 * eij * q_t[k][j]
+                                - self.regularization_param * p[i][k]
+                            )
+                            q_t[k][j] = q_t[k][j] + self.learning_rate * (
+                                2 * eij * p[i][k]
+                                - self.regularization_param * q_t[k][j]
+                            )
+            e = 0
+            for i in range(n_row):
+                for j in range(len(R[i])):
+                    if R[i][j] > 0:
+                        e = e + pow(R[i][j] - np.dot(p[i, :], q_t[:, j]), 2)
+                        for k in range(self.latent_features):
+                            e = e + (self.regularization_param / 2) * (
+                                pow(p[i][k], 2) + pow(q_t[k][j], 2)
+                            )
+            if e_current is None:
+                e_current = e
+            else:
+                if abs(e_current - e) < self.tol:
+                    fails += 1
+                else:
+                    fails = 0
+                e_current = e
+            if fails >= self.n_fail:
+                break
+        nR = np.dot(p, q_t)
+
+        # transform values per-column (i.e., only allowing values found in original)
+        tR = self.transform(R, nR)
+
+        # get accuracy of re-constructing non-missing genotypes
+        accuracy = self.accuracy(X, tR)
+
+        # insert imputed values for missing genotypes
+        fR = X
+        fR[X < 0] = tR[X < 0]
+
+        if self.verbose:
+            print("Done!")
+
+        return fR
+
+    def transform(self, original, predicted):
+        n_row = len(original)
+        n_col = len(original[0])
+        tR = predicted
+        for j in range(n_col):
+            observed = predicted[:, j]
+            expected = original[:, j]
+            options = np.unique(expected[expected != 0])
+            for i in range(n_row):
+                transform = min(options, key=lambda x: abs(x - predicted[i, j]))
+                tR[i, j] = transform
+        tR = tR - 1
+        tR[tR < 0] = -9
+        return tR
+
+    def accuracy(self, expected, predicted):
+        prop_same = np.sum(expected[expected >= 0] == predicted[expected >= 0])
+        tot = expected[expected >= 0].size
+        accuracy = prop_same / tot
+        return accuracy
+
+    def write2file(
+        self, X: pd.DataFrame | np.ndarray | List[List[int | float]]
+    ) -> None:
+        """Write imputed data to file on disk.
+
+        Args:
+            X (pandas.DataFrame | numpy.ndarray | List[List[int | float]]): Imputed data to write to file.
+
+        Raises:
+            TypeError: If X is of unsupported type.
+        """
+        outfile = Path(
+            f"{self.prefix}_output",
+            "alignments",
+            "Deterministic",
+            "ImputeMF",
+        )
+
+        Path(outfile).mkdir(parents=True, exist_ok=True)
+        outfile = Path(outfile) / "imputed_012.csv"
+
+        if isinstance(X, pd.DataFrame):
+            df = X
+        elif isinstance(X, (np.ndarray, list)):
+            df = pd.DataFrame(X)
+        else:
+            raise TypeError(
+                f"Could not write imputed data because it is of incorrect "
+                f"type. Got {type(X)}"
+            )
+
+        df.to_csv(outfile, header=False, index=False)