pertpy 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

pertpy/tools/_differential_gene_expression.py

@@ -1,325 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Literal
-
-import decoupler as dc
-import numpy as np
-import numpy.typing as npt
-import pandas as pd
-from scipy.stats import kendalltau, pearsonr, spearmanr
-from statsmodels.stats.multitest import fdrcorrection
-
-if TYPE_CHECKING:
-    from anndata import AnnData
-
-
-class DifferentialGeneExpression:
-    """Support for differential gene expression for scverse."""
-
-    def get_pseudobulk(
-        self,
-        adata: AnnData,
-        sample_col: str,
-        groups_col: str,
-        obs: pd.DataFrame = None,
-        layer: str = None,
-        use_raw: bool = False,
-        mode: str = "sum",
-        min_cells=10,
-        min_counts: int = 1000,
-        dtype: npt.DTypeLike = np.float32,
-        skip_checks: bool = False,
-    ) -> AnnData:
-        """Summarizes expression profiles across cells per sample and group.
-
-        Generates summarized expression profiles across cells per sample (e.g. sample id) and group (e.g. cell type) based on the metadata found in .obs.
-        To ensure a minimum quality control, this function removes genes that are not expressed enough across cells (min_prop) or samples (min_smpls),
-        and samples with not enough cells (min_cells) or gene counts (min_counts).
-
-        By default this function expects raw integer counts as input and sums them per sample and group (mode='sum'), but other modes are available.
-
-        This function produces some quality control metrics to assess if is necessary to filter some samples.
-        The number of cells that belong to each sample is stored in `.obs['psbulk_n_cells']`,
-        the total sum of counts per sample in .obs['psbulk_counts'], and the proportion of cells that express a given gene in `.layers[‘psbulk_props’]`.
-
-        Wraps decoupler's `get_pseudobulk` function.
-        See: https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.get_pseudobulk.html#decoupler.get_pseudobulk
-        for more details.
-
-        Args:
-            adata: Input AnnData object.
-            sample_col: Column of obs where to extract the samples names.
-            groups_col: Column of obs where to extract the groups names.
-            obs: If provided, metadata DataFrame.
-            layer: If provided, which layer to use.
-            use_raw: Use raw attribute of the AnnData object if present.
-            mode: How to perform the pseudobulk.
-                  Available options are 'sum', 'mean' or 'median'. Also accepts callback functions to perform custom aggregations.
-                  Additionally, it is also possible to provide a dictionary of different callback functions, each one stored in a different resulting `.layer`.
-                  In this case, the result of the first callback function of the dictionary is stored in .X by default.
-            min_cells: Filter to remove samples by a minimum number of cells in a sample-group pair.
-            min_counts: Filter to remove samples by a minimum number of summed counts in a sample-group pair.
-            dtype: Type of float used.
-            skip_checks: Whether to skip input checks.
-                         Set to True when working with positive and negative data, or when counts are not integers.
-
-        Returns:
-            Returns new AnnData object with unormalized pseudobulk profiles per sample and group.
-        """
-        pseudobulk_adata = dc.get_pseudobulk(
-            adata,
-            sample_col=sample_col,
-            groups_col=groups_col,
-            obs=obs,
-            layer=layer,
-            use_raw=use_raw,
-            mode=mode,
-            min_counts=min_counts,
-            dtype=dtype,
-            min_cells=min_cells,
-            skip_checks=skip_checks,
-        )
-
-        return pseudobulk_adata
-
-    def filter_by_expr(
-        self,
-        adata: AnnData,
-        obs: pd.DataFrame = None,
-        group: str | None = None,
-        lib_size: int | float | None = None,
-        min_count: int = 10,
-        min_total_count: int = 15,
-        large_n: int = 10,
-        min_prop: float = 0.7,
-    ) -> AnnData:
-        """Filter AnnData by which genes have sufficiently large counts to be retained in a statistical analysis.
-
-        Wraps decoupler's `filter_by_expr` function.
-        See https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.filter_by_expr.html#decoupler.filter_by_expr
-        for more details.
-
-        Args:
-            adata: AnnData obtained after running `get_pseudobulk`.
-            obs: Metadata dataframe, only needed if `adata` is not an `AnnData`.
-            group: Name of the `.obs` column to group by. If None, assumes all samples belong to one group.
-            lib_size: Library size. Defaults to the sum of reads per sample if None.
-            min_count: Minimum count required per gene for at least some samples.
-            min_total_count: Minimum total count required per gene across all samples.
-            large_n: Number of samples per group considered to be "large".
-            min_prop: Minimum proportion of samples in the smallest group that express the gene.
-
-        Returns:
-            AnnData with only the genes that are to be kept.
-        """
-        genes = dc.filter_by_expr(
-            adata=adata,
-            obs=obs,
-            group=group,
-            lib_size=lib_size,
-            min_count=min_count,
-            min_total_count=min_total_count,
-            large_n=large_n,
-            min_prop=min_prop,
-        )
-        filtered_adata = adata[:, genes].copy()
-
-        return filtered_adata
-
-    def filter_by_prop(self, adata: AnnData, min_prop: float = 0.2, min_samples: int = 2) -> AnnData:
-        """Determine which genes are expressed in a sufficient proportion of cells across samples.
-
-        This function selects genes that are sufficiently expressed across cells in each sample and that this condition
-        is met across a minimum number of samples.
-
-        Args:
-            adata: AnnData obtained after running `get_pseudobulk`. It requieres `.layer['psbulk_props']`.
-            min_prop: Minimum proportion of cells that express a gene in a sample.
-            min_samples: Minimum number of samples with bigger or equal proportion of cells with expression than `min_prop`.
-
-        Returns:
-            AnnData with only the genes that are to be kept.
-        """
-        genes = dc.filter_by_prop(adata=adata, min_prop=min_prop, min_smpls=min_samples)
-        filtered_adata = adata[:, genes].copy()
-
-        return filtered_adata
-
-    def calculate_correlation(
-        self,
-        de_res_1: pd.DataFrame,
-        de_res_2: pd.DataFrame,
-        method: Literal["spearman", "pearson", "kendall-tau"] = "spearman",
-    ) -> pd.DataFrame:
-        """Calculate the Spearman correlation coefficient for 'pvals_adj' and 'logfoldchanges' columns.
-
-        Args:
-            de_res_1: A DataFrame with DE result columns.
-            de_res_2: Another DataFrame with the same DE result columns.
-            method: The correlation method to apply. One of `spearman`, `pearson`, `kendall-tau`.
-                    Defaults to `spearman`.
-
-        Returns:
-            A DataFrame with the Spearman correlation coefficients for 'pvals_adj' and 'logfoldchanges'.
-        """
-        columns_of_interest = ["pvals_adj", "logfoldchanges"]
-        correlation_data = {}
-        for col in columns_of_interest:
-            match method:
-                case "spearman":
-                    correlation, _ = spearmanr(de_res_1[col], de_res_2[col])
-                case "pearson":
-                    correlation, _ = pearsonr(de_res_1[col], de_res_2[col])
-                case "kendall-tau":
-                    correlation, _ = kendalltau(de_res_1[col], de_res_2[col])
-                case _:
-                    raise ValueError("Unknown correlation method.")
-            correlation_data[col] = correlation
-
-        return pd.DataFrame([correlation_data], columns=columns_of_interest)
-
-    def calculate_jaccard_index(self, de_res_1: pd.DataFrame, de_res_2: pd.DataFrame, threshold: float = 0.05) -> float:
-        """Calculate the Jaccard index for sets of significantly expressed genes/features based on a p-value threshold.
-
-        Args:
-            de_res_1: A DataFrame with DE result columns, including 'pvals'.
-            de_res_2: Another DataFrame with the same DE result columns.
-            threshold: A threshold for determining significant expression (default is 0.05).
-
-        Returns:
-            The Jaccard index.
-        """
-        significant_set_1 = set(de_res_1[de_res_1["pvals"] <= threshold].index)
-        significant_set_2 = set(de_res_2[de_res_2["pvals"] <= threshold].index)
-
-        intersection = significant_set_1.intersection(significant_set_2)
-        union = significant_set_1.union(significant_set_2)
-
-        return len(intersection) / len(union) if union else 0
-
-    def calculate_cohens_d(self, de_res_1: pd.DataFrame, de_res_2: pd.DataFrame) -> pd.Series:
-        """Calculate Cohen's D for the logfoldchanges.
-
-        Args:
-            de_res_1: A DataFrame with DE result columns, including 'logfoldchanges'.
-            de_res_2: Another DataFrame with the same DE result columns.
-
-        Returns:
-            A pandas Series containing Cohen's D for each gene/feature.
-        """
-        means_1 = de_res_1["logfoldchanges"].mean()
-        means_2 = de_res_2["logfoldchanges"].mean()
-        sd_1 = de_res_1["logfoldchanges"].std()
-        sd_2 = de_res_2["logfoldchanges"].std()
-
-        pooled_sd = np.sqrt((sd_1**2 + sd_2**2) / 2)
-        cohens_d = (means_1 - means_2) / pooled_sd
-
-        return cohens_d
-
-    def de_res_to_anndata(
-        self,
-        adata: AnnData,
-        de_res: pd.DataFrame,
-        *,
-        groupby: str,
-        gene_id_col: str = "gene_symbols",
-        score_col: str = "scores",
-        pval_col: str = "pvals",
-        pval_adj_col: str | None = "pvals_adj",
-        lfc_col: str = "logfoldchanges",
-        key_added: str = "rank_genes_groups",
-    ) -> None:
-        """Add tabular differential expression result to AnnData as if it was produced by `scanpy.tl.rank_genes_groups`.
-
-        Args:
-            adata:
-                Annotated data matrix
-            de_res:
-                Tablular de result
-            groupby:
-                Column in `de_res` that indicates the group. This column must also exist in `adata.obs`.
-            gene_id_col:
-                Column in `de_res` that holds the gene identifiers
-            score_col:
-                Column in `de_res` that holds the score (results will be ordered by score).
-            pval_col:
-                Column in `de_res` that holds the unadjusted pvalue
-            pval_adj_col:
-                Column in `de_res` that holds the adjusted pvalue.
-                If not specified, the unadjusted pvalues will be FDR-adjusted.
-            lfc_col:
-                Column in `de_res` that holds the log fold change
-            key_added:
-                Key under which the results will be stored in `adata.uns`
-        """
-        if groupby not in adata.obs.columns or groupby not in de_res.columns:
-            raise ValueError("groupby column must exist in both adata and de_res.")
-        res_dict = {
-            "params": {
-                "groupby": groupby,
-                "reference": "rest",
-                "method": "other",
-                "use_raw": True,
-                "layer": None,
-                "corr_method": "other",
-            },
-            "names": [],
-            "scores": [],
-            "pvals": [],
-            "pvals_adj": [],
-            "logfoldchanges": [],
-        }
-        df_groupby = de_res.groupby(groupby)
-        for _, tmp_df in df_groupby:
-            tmp_df = tmp_df.sort_values(score_col, ascending=False)
-            res_dict["names"].append(tmp_df[gene_id_col].values)  # type: ignore
-            res_dict["scores"].append(tmp_df[score_col].values)  # type: ignore
-            res_dict["pvals"].append(tmp_df[pval_col].values)  # type: ignore
-            if pval_adj_col is not None:
-                res_dict["pvals_adj"].append(tmp_df[pval_adj_col].values)  # type: ignore
-            else:
-                res_dict["pvals_adj"].append(fdrcorrection(tmp_df[pval_col].values)[1])  # type: ignore
-            res_dict["logfoldchanges"].append(tmp_df[lfc_col].values)  # type: ignore
-
-        for key in ["names", "scores", "pvals", "pvals_adj", "logfoldchanges"]:
-            res_dict[key] = pd.DataFrame(
-                np.vstack(res_dict[key]).T,
-                columns=list(df_groupby.groups.keys()),
-            ).to_records(index=False, column_dtypes="O")
-        adata.uns[key_added] = res_dict
-
-    def de_analysis(
-        self,
-        adata: AnnData,
-        groupby: str,
-        method: Literal["t-test", "wilcoxon", "pydeseq2", "deseq2", "edger"],
-        *formula: str | None,
-        contrast: str | None,
-        inplace: bool = True,
-        key_added: str | None,
-    ) -> pd.DataFrame:
-        """Perform differential expression analysis.
-
-        Args:
-            adata: single-cell or pseudobulk AnnData object
-            groupby: Column in adata.obs that contains the factor to test, e.g. `treatment`.
-                     For simple statistical tests (t-test, wilcoxon), it is sufficient to specify groupby.
-                     Linear models require to specify a formula.
-                     In that case, the `groupby` column is used to compute the contrast.
-            method: Which method to use to perform the DE test.
-            formula: model specification for linear models. E.g. `~ treatment + sex + age`.
-                     MUST contain the factor specified in `groupby`.
-            contrast: See e.g. https://www.statsmodels.org/devel/contrasts.html for more information.
-            inplace: if True, save the result in `adata.varm[key_added]`
-            key_added: Key under which the result is saved in `adata.varm` if inplace is True.
-                       If set to None this defaults to `de_{method}_{groupby}`.
-        Returns:
-            Depending on the method a Pandas DataFrame containing at least:
-            * gene_id
-            * log2 fold change
-            * mean expression
-            * unadjusted p-value
-            * adjusted p-value
-        """
-        raise NotImplementedError

pertpy-0.7.0.dist-info/RECORD

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