Merge pull request #665 from Sichao25/shiny

Extra filter after pearson residuals normalization

dynamo/preprocessing/Preprocessor.py

@@ -30,7 +30,7 @@
 from .QC import basic_stats
 from .QC import filter_cells_by_outliers as monocle_filter_cells_by_outliers
 from .QC import filter_genes_by_outliers as monocle_filter_genes_by_outliers
-from .QC import regress_out_parallel
+from .QC import regress_out_parallel, filter_cells_by_highly_variable_genes
 from .transform import Freeman_Tukey, log, log1p, log2
 from .utils import (
     _infer_labeling_experiment_type,
@@ -52,6 +52,8 @@ def __init__(
         filter_cells_by_outliers_kwargs: Dict[str, Any] = {},
         filter_genes_by_outliers_function: Callable = monocle_filter_genes_by_outliers,
         filter_genes_by_outliers_kwargs: Dict[str, Any] = {},
+        filter_cells_by_highly_variable_genes_function: Callable = filter_cells_by_highly_variable_genes,
+        filter_cells_by_highly_variable_genes_kwargs: Dict[str, Any] = {},
         normalize_by_cells_function: Callable = normalize,
         normalize_by_cells_function_kwargs: Dict[str, Any] = {},
         size_factor_function: Callable = calc_sz_factor,
@@ -88,6 +90,10 @@ def __init__(
             filter_cells_by_outliers_kwargs: arguments that will be passed to filter_cells_by_outliers. Defaults to {}.
             filter_genes_by_outliers_function: filter genes by thresholds. Defaults to monocle_filter_genes_by_outliers.
             filter_genes_by_outliers_kwargs: arguments that will be passed to filter_genes_by_outliers. Defaults to {}.
+            filter_cells_by_highly_variable_genes_function: filter cells by highly variable genes. Defaults to
+                filter_cells_by_highly_variable_genes.
+            filter_cells_by_highly_variable_genes_kwargs: arguments that will be passed to
+                filter_cells_by_highly_variable_genes. Defaults to {}.
             normalize_by_cells_function: function for performing cell-wise normalization. Defaults to
                 normalize_cell_expr_by_size_factors.
             normalize_by_cells_function_kwargs: arguments that will be passed to normalize_by_cells_function. Defaults
@@ -117,6 +123,7 @@ def __init__(
 
         self.filter_cells_by_outliers = filter_cells_by_outliers_function
         self.filter_genes_by_outliers = filter_genes_by_outliers_function
+        self.filter_cells_by_highly_variable_genes = filter_cells_by_highly_variable_genes_function
         self.normalize_by_cells = normalize_by_cells_function
         self.calc_size_factor = size_factor_function
         self.calc_new_to_total_ratio = calc_new_to_total_ratio
@@ -135,6 +142,7 @@ def __init__(
 
         # kwargs pass to the functions above
         self.filter_genes_by_outliers_kwargs = filter_genes_by_outliers_kwargs
+        self.filter_cells_by_highly_variable_genes_kwargs = filter_cells_by_highly_variable_genes_kwargs
         self.normalize_by_cells_function_kwargs = normalize_by_cells_function_kwargs
         self.filter_cells_by_outliers_kwargs = filter_cells_by_outliers_kwargs
         self.size_factor_kwargs = size_factor_kwargs
@@ -283,6 +291,18 @@ def _filter_genes_by_outliers(self, adata: AnnData) -> None:
             main_debug("gene filter kwargs:" + str(self.filter_genes_by_outliers_kwargs))
             self.filter_genes_by_outliers(adata, **self.filter_genes_by_outliers_kwargs)
 
+    def _filter_cells_by_highly_variable_genes(self, adata: AnnData) -> None:
+        """Select valid cells based on the method specified as the preprocessor's `filter_cells_by_highly_variable_genes`.
+
+        Args:
+            adata: an AnnData object.
+        """
+
+        if self.filter_cells_by_highly_variable_genes:
+            main_debug("filtering cells by highly variable genes...")
+            main_debug("filter_cells_by_highly_variable_genes kwargs:" + str(self.filter_cells_by_highly_variable_genes_kwargs))
+            self.filter_cells_by_highly_variable_genes(adata, **self.filter_cells_by_highly_variable_genes_kwargs)
+
     def _calc_size_factor(self, adata: AnnData) -> None:
         """Calculate the size factor of each cell based on method specified as the preprocessor's `calc_size_factor`.
 
@@ -692,6 +712,7 @@ def config_pearson_residuals_recipe(self, adata: AnnData) -> None:
 
         self.filter_cells_by_outliers = None
         self.filter_genes_by_outliers = None
+        self.filter_cells_by_highly_variable_genes_kwargs = {"keep_filtered": False}
         self.normalize_by_cells = None
         self.select_genes = select_genes_by_pearson_residuals
         self.select_genes_kwargs = {"n_top_genes": 2000}
@@ -730,6 +751,7 @@ def preprocess_adata_pearson_residuals(
         self._exclude_gene_list(adata)
         self._force_gene_list(adata)
 
+        self._filter_cells_by_highly_variable_genes(adata)
         self._normalize_selected_genes(adata)
         if len(self.regress_out_kwargs["obs_keys"]) > 0:
             self._regress_out(adata)
@@ -751,6 +773,7 @@ def config_monocle_pearson_residuals_recipe(self, adata: AnnData) -> None:
         self.config_monocle_recipe(adata)
         # self.filter_cells_by_outliers = None
         # self.filter_genes_by_outliers = None
+        self.filter_cells_by_highly_variable_genes_kwargs = {"keep_filtered": False}
         self.normalize_by_cells = normalize
         self.select_genes = select_genes_by_pearson_residuals
         self.select_genes_kwargs = {"n_top_genes": 2000}
@@ -791,6 +814,7 @@ def preprocess_adata_monocle_pearson_residuals(
         self._calc_size_factor(adata)
         self._normalize_by_cells(adata)
         adata.X = X_copy
+        self._filter_cells_by_highly_variable_genes(adata)
         self._normalize_selected_genes(adata)
         if len(self.regress_out_kwargs["obs_keys"]) > 0:
             self._regress_out(adata)

dynamo/preprocessing/QC.py

@@ -270,6 +270,48 @@ def filter_cells_by_outliers(
     return adata
 
 
+def filter_cells_by_highly_variable_genes(
+    adata: anndata.AnnData,
+    keep_filtered: bool = False,
+    select_genes_layer: str = DKM.X_LAYER,
+    high_var_genes_key: str = DKM.VAR_USE_FOR_PCA,
+    obs_store_key: str = "pass_basic_filter",
+) -> anndata.AnnData:
+    """Filter cells based on the expression of highly variable genes.
+
+    Args:
+        adata: an AnnData object.
+        keep_filtered: whether to keep cells that don't pass the filtering in the adata object.
+        select_genes_layer: the layer used for genes selection.
+        high_var_genes_key: the key in adata.var to store the highly variable genes.
+        obs_store_key: the key in adata.obs to store the filtered data.
+
+    Returns:
+        An updated AnnData object indicating the selection of cells for downstream analysis.
+    """
+    if high_var_genes_key not in adata.var.keys():
+        raise ValueError(
+            "The key %s is not found in adata.var. Please run genes selection methods first."
+            % high_var_genes_key
+        )
+
+    if obs_store_key not in adata.obs.keys():
+        adata.obs[obs_store_key] = True
+
+    filter_bool = adata.var[high_var_genes_key].values
+    X = DKM.select_layer_data(adata, layer=select_genes_layer)
+    X = X[:, filter_bool].A if issparse(X) else X[:, filter_bool]
+    nan_columns_index = np.where(np.sum(X, axis=1) == 0)[0]
+
+    adata.obs[obs_store_key].iloc[nan_columns_index] = False
+
+    if not keep_filtered:
+        main_debug("inplace subsetting adata by filtered cells", indent_level=2)
+        adata._inplace_subset_obs(adata.obs[obs_store_key])
+
+    return adata
+
+
 def filter_genes_by_outliers(
     adata: anndata.AnnData,
     filter_bool: Union[np.ndarray, None] = None,

dynamo/preprocessing/__init__.py

@@ -15,6 +15,7 @@
     basic_stats,
     filter_genes_by_clusters,
     filter_cells_by_outliers,
+    filter_cells_by_highly_variable_genes,
     filter_genes_by_outliers,
     filter_genes_by_pattern,
 )
@@ -59,6 +60,7 @@
     "recipe_velocyto",
     "calc_Gini",
     "filter_cells_by_outliers",
+    "filter_cells_by_highly_variable_genes",
     "select_genes_monocle",
     "select_genes_by_pearson_residuals",
     "filter_genes",