DeConveil 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl

deconveil/ds.py

@@ -132,16 +132,16 @@ class deconveil_stats:
     def __init__(
         self,
         dds: deconveil_fit,
-        contrast: Optional[List[str]] = None,
+        contrast: list[str] | np.ndarray,
         alpha: float = 0.05,
         cooks_filter: bool = True,
         independent_filter: bool = True,
-        prior_LFC_var: Optional[np.ndarray] = None,
+        prior_LFC_var: np.ndarray | None = None,
         lfc_null: float = 0.0,
-        alt_hypothesis: Optional[
-            Literal["greaterAbs", "lessAbs", "greater", "less"]
-        ] = None,
-        inference: Optional[Inference] = None,
+        alt_hypothesis: (
+            Literal["greaterAbs", "lessAbs", "greater", "less"] | None
+        ) = None,
+        inference: Inference | None = None,
         quiet: bool = False,
     ) -> None:
         assert (
@@ -164,24 +164,67 @@ class deconveil_stats:
         self.lfc_null = lfc_null
         self.alt_hypothesis = alt_hypothesis
 
-        # Check the validity of the contrast (if provided) or build it.
-        self._build_contrast(contrast)
-
         # Initialize the design matrix and LFCs. If the chosen reference level are the
         # same as in dds, keep them unchanged. Otherwise, change reference level.
         self.design_matrix = self.dds.obsm["design_matrix"].copy()
         self.LFC = self.dds.varm["LFC"].copy()
 
-        # Build a contrast vector corresponding to the variable and levels of interest
-        self._build_contrast_vector()
-
+        # Check the validity of the contrast (if provided) or build it.
+        self.contrast: list[str] | np.ndarray
+        if contrast is None:
+            raise ValueError(
+                """Default contrasts are no longer supported.
+                The "contrast" argument must be provided."""
+            )
+        elif isinstance(contrast, np.ndarray):
+            if contrast.shape[0] != self.dds.obsm["design_matrix"].shape[1]:
+                raise ValueError(
+                    "The contrast vector must have the same length as the design matrix."
+                )
+            self.contrast = contrast
+            self.contrast_vector = contrast
+        else:
+            self.contrast = contrast
+            self._build_contrast_vector()
+            
         # Set a flag to indicate that LFCs are unshrunk
         self.shrunk_LFCs = False
         self.quiet = quiet
 
+        if inference:
+            if n_cpus:
+                if hasattr(inference, "n_cpus"):
+                    inference.n_cpus = n_cpus
+                else:
+                    warnings.warn(
+                        "The provided inference object does not have an n_cpus "
+                        "attribute, cannot override `n_cpus`.",
+                        UserWarning,
+                        stacklevel=2,
+                    )
+
         # Initialize the inference object.
         self.inference = inference or DefInference()
 
+        # If the `refit_cooks` attribute of the dds object is True, check that outliers
+        # were actually refitted.
+        #if self.dds.refit_cooks and "replaced" not in self.dds.var:
+            #raise AttributeError(
+                #"dds has 'refit_cooks' set to True but Cooks outliers have not been "
+                #"refitted. Please run 'dds.refit()' first or set 'dds.refit_cooks' "
+                #"to False."
+            #)
+        if self.dds.refit_cooks and "replaced" not in getattr(self.dds, "varm", {}):
+            raise AttributeError(
+                "dds has 'refit_cooks' set to True but Cooks outliers have not been "
+                "refitted. Please run 'dds.refit()' first or set 'dds.refit_cooks' "
+                "to False."
+            )
+
+    @property
+    def variables(self):
+        """Get the names of the variables used in the model definition."""
+        return self.dds.variables
         
     def summary(
         self,
@@ -249,9 +292,12 @@ class deconveil_stats:
         self.results_df["padj"] = self.padj
 
         if not self.quiet:
-            if self.contrast[1] == self.contrast[2] == "":
-                # The factor is continuous
-                print(f"Log2 fold change & Wald test p-value: " f"{self.contrast[0]}")
+            if isinstance(self.contrast, np.ndarray):
+                # The contrast vector was directly provided
+                print(
+                    "Log2 fold change & Wald test p-value, contrast vector: "
+                    f"{self.contrast}"
+                )
             else:
                 # The factor is categorical
                 print(
@@ -259,6 +305,7 @@ class deconveil_stats:
                     f"{self.contrast[0]} {self.contrast[1]} vs {self.contrast[2]}"
                 )
             print(self.results_df)
+            
 
     def run_wald_test(self) -> None:
         """Perform a Wald test.
@@ -288,7 +335,7 @@ class deconveil_stats:
             ridge_factor = np.diag(1 / self.prior_LFC_var**2)
         else:
             ridge_factor = np.diag(np.repeat(1e-6, num_vars))
-
+        
         design_matrix = self.design_matrix.values
         LFCs = self.LFC.values
 
@@ -320,70 +367,38 @@ class deconveil_stats:
             self.p_values.loc[self.dds.new_all_zeroes_genes] = 1.0
 
 
-    def lfc_shrink(self, coeff: Optional[str] = None, adapt: bool = True) -> None:
+    def lfc_shrink(self, coeff: str, adapt: bool = True) -> None:
         """LFC shrinkage with an apeGLM prior :cite:p:`DeseqStats-zhu2019heavy`.
 
         Shrinks LFCs using a heavy-tailed Cauchy prior, leaving p-values unchanged.
 
         Parameters
         ----------
-        coeff : str or None
-            The LFC coefficient to shrink. If set to ``None``, the method will try to
-            shrink the coefficient corresponding to the ``contrast`` attribute.
-            If the desired coefficient is not available, it may be set from the
-            :class:`pydeseq2.dds.DeseqDataSet` argument ``ref_level``.
+        coeff : str
+            The LFC coefficient to shrink. Must be one of the columns of the LFC matrix.
             (default: ``None``).
+            
         adapt: bool
             Whether to use the MLE estimates of LFC to adapt the prior. If False, the
             prior scale is set to 1. (``default=True``)
         """
-        if self.contrast[1] == self.contrast[2] == "":
-            # The factor being tested is continuous
-            contrast_level = self.contrast[0]
-        else:
-            # The factor being tested is categorical
-            contrast_level = (
-                f"{self.contrast[0]}_{self.contrast[1]}_vs_{self.contrast[2]}"
-            )
 
-        if coeff is not None:
-            if coeff not in self.LFC.columns:
-                split_coeff = coeff.split("_")
-                if len(split_coeff) == 4:
-                    raise KeyError(
-                        f"The coeff argument '{coeff}' should be one the LFC columns. "
-                        f"The available LFC coeffs are {self.LFC.columns[1:]}. "
-                        f"If the desired coefficient is not available, please set "
-                        f"`ref_level = [{split_coeff[0]}, {split_coeff[3]}]` "
-                        f"in DeseqDataSet and rerun."
-                    )
-                else:
-                    raise KeyError(
-                        f"The coeff argument '{coeff}' should be one the LFC columns. "
-                        f"The available LFC coeffs are {self.LFC.columns[1:]}. "
-                        f"If the desired coefficient is not available, please set the "
-                        f"appropriate`ref_level` in DeseqDataSet and rerun."
-                    )
-        elif contrast_level not in self.LFC.columns:
+        if coeff not in self.LFC.columns:
             raise KeyError(
-                f"lfc_shrink's coeff argument was set to None, but the coefficient "
-                f"corresponding to the contrast {self.contrast} is not available."
-                f"The available LFC coeffs are {self.LFC.columns[1:]}. "
-                f"If the desired coefficient is not available, please set "
-                f"`ref_level = [{self.contrast[0]}, {self.contrast[2]}]` "
-                f"in DeseqDataSet and rerun."
-            )
-        else:
-            coeff = contrast_level
+                f"coeff '{coeff}' must be one of the LFC columns.\n"
+                f"Available: {list(self.LFC.columns)}"
+        )
 
         coeff_idx = self.LFC.columns.get_loc(coeff)
 
+        design_matrix = self.design_matrix.values
         size = 1.0 / self.dds.varm["dispersions"]
-        offset = np.log(self.dds.obsm["size_factors"]) 
+        offset = np.log(self.dds.obsm["size_factors"])
         
         counts=self.dds.data["counts"]
         cnv=self.dds.data["cnv"].to_numpy()
-        cnv = cnv + 0.1
+        cnv = (cnv / 2) + 0.1 
+        #cnv = cnv + 0.1
         cnv = np.log(cnv)      
 
         # Set priors
@@ -444,24 +459,10 @@ class deconveil_stats:
         if hasattr(self, "results_df"):
             self.results_df["log2FoldChange"] = self.LFC.iloc[:, coeff_idx] / np.log(2)
             self.results_df["lfcSE"] = self.SE / np.log(2)
-            # Get the corresponding factor, tested and reference levels of the shrunk
-            # coefficient
-            split_coeff = coeff.split("_")
-            # Categorical coeffs are of the form "factor_A_vs_B", and continuous coeffs
-            # of the form "factor".
-            if len(split_coeff) == 1:
-                # The factor is continuous
-                print(f"Shrunk log2 fold change & Wald test p-value: " f"{coeff}")
-            else:
-                # The factor is categorical
-                # Categorical coeffs are of the form "factor_A_vs_B", hence "factor"
-                # is split_coeff[0], "A" is split_coeff[1] and "B" split_coeff[3]
-                print(
-                    f"Shrunk log2 fold change & Wald test p-value: "
-                    f"{split_coeff[0]} {split_coeff[1]} vs {split_coeff[3]}"
-                )
+            if not self.quiet:
+                print(f"Shrunk log2 fold change & Wald test p-value: {coeff}")
+                print(self.results_df)
 
-            print(self.results_df)
 
 
     def _independent_filtering(self) -> None:
@@ -534,7 +535,6 @@ class deconveil_stats:
 
         # As in DESeq2, only take samples with 3 or more replicates when looking for
         # max cooks.
-        #use_for_max = n_or_more_replicates(self.design_matrix, 3)
         use_for_max = n_or_more_replicates(self.dds.obsm["design_matrix"], 3).values
 
         # If for a gene there are 3 samples or more that have more counts than the
@@ -614,70 +614,7 @@ class deconveil_stats:
             return min_var
         else:
             return root_scalar(objective, bracket=[min_var, max_var]).root
-
-    def _build_contrast(self, contrast: Optional[List[str]] = None) -> None:
-        """Check the validity of the contrast (if provided).
-
-        If not, build a default
-        contrast, corresponding to the last column of the design matrix.
-        A contrast should be a list of three strings, in the following format:
-        ``['variable_of_interest', 'tested_level', 'reference_level']``.
-        Names must correspond to the metadata data passed to the DeseqDataSet.
-        E.g., ``['condition', 'B', 'A']`` will measure the LFC of 'condition B'
-        compared to 'condition A'.
-        For continuous variables, the last two strings will be left empty, e.g.
-        ``['measurement', '', ''].
-        If None, the last variable from the design matrix
-        is chosen as the variable of interest, and the reference level is picked
-        alphabetically.
-
-        Parameters
-        ----------
-        contrast : list or None
-            A list of three strings, in the following format:
-            ``['variable_of_interest', 'tested_level', 'reference_level']``.
-            (default: ``None``).
-        """
-        if contrast is not None:  # Test contrast if provided
-            if len(contrast) != 3:
-                raise ValueError("The contrast should contain three strings.")
-            if contrast[0] not in self.dds.design_factors:
-                raise KeyError(
-                    f"The contrast variable ('{contrast[0]}') should be one "
-                    f"of the design factors."
-                )
-            if not (contrast[1] == contrast[2] == ""):
-                # The contrast factor is categorical, so we should check that the tested
-                # and reference levels are valid.
-                if contrast[1] not in self.dds.obs[contrast[0]].values:
-                    raise KeyError(
-                        f"The tested level ('{contrast[1]}') should correspond to "
-                        f"one of the levels of '{contrast[0]}'"
-                    )
-                if contrast[2] not in self.dds.obs[contrast[0]].values:
-                    raise KeyError(
-                        f"The reference level ('{contrast[2]}') should correspond to "
-                        f"one of the levels of '{contrast[0]}'"
-                    )
-            self.contrast = contrast
-        else:  # Build contrast if None
-            factor = self.dds.design_factors[-1]
-            # Check whether this factor is categorical or continuous.
-            if (
-                self.dds.continuous_factors is not None
-                and factor in self.dds.continuous_factors
-            ):
-                # The factor is continuous
-                self.contrast = [factor, "", ""]
-            else:
-                # The factor is categorical
-                factor_col = next(
-                    col
-                    for col in self.dds.obsm["design_matrix"].columns
-                    if col.startswith(factor)
-                )
-                split_col = factor_col.split("_")
-                self.contrast = [split_col[0], split_col[1], split_col[-1]]
+  
 
     def _build_contrast_vector(self) -> None:
         """
@@ -688,34 +625,9 @@ class deconveil_stats:
         factor = self.contrast[0]
         alternative = self.contrast[1]
         ref = self.contrast[2]
-        if ref == alternative == "":
-            # "factor" is a continuous variable
-            contrast_level = factor
-        else:
-            contrast_level = f"{factor}_{alternative}_vs_{ref}"
-
-        self.contrast_vector = np.zeros(self.LFC.shape[-1])
-        if contrast_level in self.design_matrix.columns:
-            self.contrast_idx = self.LFC.columns.get_loc(contrast_level)
-            self.contrast_vector[self.contrast_idx] = 1
-        elif f"{factor}_{ref}_vs_{alternative}" in self.design_matrix.columns:
-            # Reference and alternative are inverted
-            self.contrast_idx = self.LFC.columns.get_loc(
-                f"{factor}_{ref}_vs_{alternative}"
-            )
-            self.contrast_vector[self.contrast_idx] = -1
-        else:
-            # Need to change reference
-            # Get any column corresponding to the desired factor and extract old ref
-            old_ref = next(
-                col for col in self.LFC.columns if col.startswith(factor)
-            ).split("_vs_")[-1]
-            new_alternative_idx = self.LFC.columns.get_loc(
-                f"{factor}_{alternative}_vs_{old_ref}"
-            )
-            new_ref_idx = self.LFC.columns.get_loc(f"{factor}_{ref}_vs_{old_ref}")
-            self.contrast_vector[new_alternative_idx] = 1
-            self.contrast_vector[new_ref_idx] = -1
+        self.contrast_vector = self.dds.contrast(
+            column=factor, baseline=ref, group_to_compare=alternative
+        )
 
     
     def plot_MA(self, log: bool = True, save_path: Optional[str] = None, **kwargs):

deconveil/grid_search.py

@@ -67,6 +67,7 @@ def grid_fit_beta(
             raise ValueError("Beta is not properly initialized or has an unexpected shape.")
 
             
+        #mu = np.maximum(size_factors[:, None] * np.exp(design_matrix @ beta.T), min_mu)
         mu = np.maximum(cnv * size_factors[:, None] * np.exp(design_matrix @ beta.T), min_mu)
         return vec_nb_nll(counts, mu, disp) + 0.5 * (1e-6 * beta**2).sum(1)
 

deconveil/inference.py

@@ -261,9 +261,9 @@ class Inference(ABC):
         ridge_factor: np.ndarray,
         contrast: np.ndarray,
         lfc_null: np.ndarray,
-        alt_hypothesis: Optional[
-            Literal["greaterAbs", "lessAbs", "greater", "less"]
-        ] = None,
+        alt_hypothesis: (
+            Literal["greaterAbs", "lessAbs", "greater", "less"] | None
+        ) = None,
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         """Run Wald test for differential expression.
 
@@ -320,7 +320,7 @@ class Inference(ABC):
         prior_scale: float,
         optimizer: str,
         shrink_index: int,
-    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray, np.ndarray]:
         """Fit a negative binomial MAP LFC using an apeGLM prior.
 
         Only the LFC is shrinked, and not the intercept.