pertpy 0.9.5__py3-none-any.whl → 0.11.0__py3-none-any.whl

pertpy/tools/_milo.py

@@ -51,14 +51,16 @@ class Milo:
         Args:
             input: AnnData
             feature_key: Key to store the cell-level AnnData object in the MuData object
+
         Returns:
-            MuData: MuData object with original AnnData.
+            :class:`mudata.MuData` object with original AnnData.
 
         Examples:
             >>> import pertpy as pt
             >>> adata = pt.dt.bhattacherjee()
             >>> milo = pt.tl.Milo()
             >>> mdata = milo.load(adata)
+
         """
         mdata = MuData({feature_key: input, "milo": AnnData()})
 
@@ -113,6 +115,7 @@ class Milo:
             >>> mdata = milo.load(adata)
             >>> sc.pp.neighbors(mdata["rna"])
             >>> milo.make_nhoods(mdata["rna"])
+
         """
         if isinstance(data, MuData):
             adata = data[feature_key]
@@ -177,10 +180,7 @@ class Milo:
         adata.obs["nhood_ixs_random"] = adata.obs["nhood_ixs_random"].astype("int")
         adata.uns["nhood_neighbors_key"] = neighbors_key
         # Store distance to K-th nearest neighbor (used for spatial FDR correction)
-        if neighbors_key is None:
-            knn_dists = adata.obsp["distances"]
-        else:
-            knn_dists = adata.obsp[neighbors_key + "_distances"]
+        knn_dists = adata.obsp["distances"] if neighbors_key is None else adata.obsp[neighbors_key + "_distances"]
 
         nhood_ixs = adata.obs["nhood_ixs_refined"] == 1
         dist_mat = knn_dists[np.asarray(nhood_ixs), :]
@@ -223,6 +223,7 @@ class Milo:
             >>> sc.pp.neighbors(mdata["rna"])
             >>> milo.make_nhoods(mdata["rna"])
             >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
+
         """
         if isinstance(data, MuData):
             adata = data[feature_key]
@@ -297,6 +298,7 @@ class Milo:
             >>> milo.make_nhoods(mdata["rna"])
             >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
             >>> milo.da_nhoods(mdata, design="~label")
+
         """
         try:
             sample_adata = mdata["milo"]
@@ -428,7 +430,7 @@ class Milo:
             feature_key: If input data is MuData, specify key to cell-level AnnData object.
 
         Returns:
-            None. Adds in place:
+            Adds in place.
             - `milo_mdata['milo'].var["nhood_annotation"]`: assigning a label to each nhood
             - `milo_mdata['milo'].var["nhood_annotation_frac"]` stores the fraciton of cells in the neighbourhood with the assigned label
             - `milo_mdata['milo'].varm['frac_annotation']`: stores the fraction of cells from each label in each nhood
@@ -444,6 +446,7 @@ class Milo:
             >>> milo.make_nhoods(mdata["rna"])
             >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
             >>> milo.annotate_nhoods(mdata, anno_col="cell_type")
+
         """
         try:
             sample_adata = mdata["milo"]
@@ -482,7 +485,7 @@ class Milo:
             feature_key: If input data is MuData, specify key to cell-level AnnData object.
 
         Returns:
-            None. Adds in place:
+            Adds in place.
             - `milo_mdata['milo'].var["nhood_{anno_col}"]`: assigning a continuous value to each nhood
 
         Examples:
@@ -567,7 +570,7 @@ class Milo:
         sample_adata.obs = sample_obs.loc[sample_adata.obs_names]
 
     def build_nhood_graph(self, mdata: MuData, basis: str = "X_umap", feature_key: str | None = "rna"):
-        """Build graph of neighbourhoods used for visualization of DA results
+        """Build graph of neighbourhoods used for visualization of DA results.
 
         Args:
             mdata: MuData object
@@ -625,6 +628,7 @@ class Milo:
             >>> milo.make_nhoods(mdata["rna"])
             >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
             >>> milo.add_nhood_expression(mdata)
+
         """
         try:
             sample_adata = mdata["milo"]
@@ -652,7 +656,7 @@ class Milo:
     def _setup_rpy2(
         self,
     ):
-        """Set up rpy2 to run edgeR"""
+        """Set up rpy2 to run edgeR."""
         from rpy2.robjects import numpy2ri, pandas2ri
         from rpy2.robjects.packages import importr
 
@@ -715,7 +719,7 @@ class Milo:
         sample_adata.var.loc[keep_nhoods, "SpatialFDR"] = adjp
 
     @_doc_params(common_plot_args=doc_common_plot_args)
-    def plot_nhood_graph(
+    def plot_nhood_graph(  # pragma: no cover # noqa: D417
         self,
         mdata: MuData,
         *,
@@ -727,11 +731,10 @@ class Milo:
         color_map: Colormap | str | None = None,
         palette: str | Sequence[str] | None = None,
         ax: Axes | None = None,
-        show: bool = True,
         return_fig: bool = False,
         **kwargs,
     ) -> Figure | None:
-        """Visualize DA results on abstracted graph (wrapper around sc.pl.embedding)
+        """Visualize DA results on abstracted graph (wrapper around sc.pl.embedding).
 
         Args:
             mdata: MuData object
@@ -803,14 +806,13 @@ class Milo:
             **kwargs,
         )
 
-        if show:
-            plt.show()
         if return_fig:
             return fig
+        plt.show()
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
-    def plot_nhood(
+    def plot_nhood(  # pragma: no cover # noqa: D417
         self,
         mdata: MuData,
         ix: int,
@@ -820,7 +822,6 @@ class Milo:
         color_map: Colormap | str | None = None,
         palette: str | Sequence[str] | None = None,
         ax: Axes | None = None,
-        show: bool = True,
         return_fig: bool = False,
         **kwargs,
     ) -> Figure | None:
@@ -866,14 +867,13 @@ class Milo:
             **kwargs,
         )
 
-        if show:
-            plt.show()
         if return_fig:
             return fig
+        plt.show()
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
-    def plot_da_beeswarm(
+    def plot_da_beeswarm(  # pragma: no cover # noqa: D417
         self,
         mdata: MuData,
         *,
@@ -882,10 +882,9 @@ class Milo:
         alpha: float = 0.1,
         subset_nhoods: list[str] = None,
         palette: str | Sequence[str] | dict[str, str] | None = None,
-        show: bool = True,
         return_fig: bool = False,
     ) -> Figure | None:
-        """Plot beeswarm plot of logFC against nhood labels
+        """Plot beeswarm plot of logFC against nhood labels.
 
         Args:
             mdata: MuData object
@@ -994,21 +993,19 @@ class Milo:
         plt.legend(loc="upper left", title=f"< {int(alpha * 100)}% SpatialFDR", bbox_to_anchor=(1, 1), frameon=False)
         plt.axvline(x=0, ymin=0, ymax=1, color="black", linestyle="--")
 
-        if show:
-            plt.show()
         if return_fig:
             return plt.gcf()
+        plt.show()
         return None
 
     @_doc_params(common_plot_args=doc_common_plot_args)
-    def plot_nhood_counts_by_cond(
+    def plot_nhood_counts_by_cond(  # pragma: no cover # noqa: D417
         self,
         mdata: MuData,
         test_var: str,
         *,
         subset_nhoods: list[str] = None,
         log_counts: bool = False,
-        show: bool = True,
         return_fig: bool = False,
     ) -> Figure | None:
         """Plot boxplot of cell numbers vs condition of interest.
@@ -1050,8 +1047,7 @@ class Milo:
         plt.xticks(rotation=90)
         plt.xlabel(test_var)
 
-        if show:
-            plt.show()
         if return_fig:
             return plt.gcf()
+        plt.show()
         return None