mod_docstrings6

src/troutpy/pl/plotting.py

@@ -627,7 +627,7 @@ def spatial_interactions(
     figsize (Tuple[float, float]): The dimensions of the plot in inches.
     dpi (Optional[int]): The resolution (dots per inch) for the plot.
     save (Optional[Union[str, Path]]): The path to save the plot image. If `None`, the plot is displayed but not saved.
-    **kwargs : Any additional arguments passed to the `scatter` or `imshow` functions for customizing plot appearance.
+    kwargs : Any additional arguments passed to the `scatter` or `imshow` functions for customizing plot appearance.
 
     Returns:
     None
@@ -683,7 +683,7 @@ def interactions_with_arrows(
 ):
     """
     The function plots arrows from source to target cells based on transcript proximity, color-coding source and target cells, and transcript locations. An optional image layer can be overlaid behind the plot.
-    
+
     Parameters:
     - sdata (AnnData): The AnnData object containing the spatial omics data.
     - layer (str, optional): The key in `sdata` for the extracellular transcript layer to analyze. Default is 'extracellular_transcripts_enriched'.
@@ -704,13 +704,11 @@ def interactions_with_arrows(
     - figsize (Tuple[float, float], optional): Size of the plot. Default is (10, 10).
     - dpi (Optional[int], optional): Resolution of the plot. Default is 100.
     - save (Optional[Union[str, Path]], optional): If provided, the path where the plot will be saved.
-    - **kwargs: Additional arguments passed to the `scatter` and `imshow` functions for customization.
+    - kwargs: Additional arguments passed to the `scatter` and `imshow` functions for customization.
 
     Returns:
     - None: The function displays or saves a plot of interactions between cells and transcripts.
 
-    Notes:
-    The plot will show arrows from source to target cells, with different colors for source, target, and transcript points.
     """ 
     # Extract relevant data
     transcripts = sdata.points[layer]

src/troutpy/tl/segmentation_free.py

@@ -18,19 +18,19 @@ def segmentation_free_clustering(
     This function clusters transcriptomic data without relying on pre-defined cell or tissue segmentations.It supports multiple clustering methods, with Points2Regions being the default.
 
     Parameters:
-    - sdata (SpatialData): A spatial data object containing transcriptomic information.
-    - params (dict): A dictionary of parameters for the selected clustering method.For `points2regions`:
-        - 'num_clusters' (int): Number of clusters (default: 300).
-        - 'pixel_width' (float): Pixel width parameter (default: 0.4).
-        - 'pixel_smoothing' (float): Pixel smoothing parameter (default: 3.5).
-    - x (str): Column name for the x-coordinates of transcripts.
-    - y (str): Column name for the y-coordinates of transcripts.
-    - feature_name (str): Column name for the feature names.
-    - method (str, optional): Clustering method to use. Options:
-        - 'points2regions': Uses the Points2Regions algorithm for clustering.
-        - 'sainsc': Placeholder for another clustering method.
-    - transcript_id (str, optional): Column name for the transcript IDs.
-    - copy (bool): If True, returns a copy of the clustering results. If False, updates `sdata` in-place.
+    sdata (SpatialData): A spatial data object containing transcriptomic information.
+    params (dict): A dictionary of parameters for the selected clustering method.For `points2regions`:
+    - 'num_clusters' (int): Number of clusters (default: 300).
+    - 'pixel_width' (float): Pixel width parameter (default: 0.4).
+    - 'pixel_smoothing' (float): Pixel smoothing parameter (default: 3.5).
+    x (str): Column name for the x-coordinates of transcripts.
+    y (str): Column name for the y-coordinates of transcripts.
+    feature_name (str): Column name for the feature names.
+    method (str, optional): Clustering method to use. Options:
+    - 'points2regions': Uses the Points2Regions algorithm for clustering.
+    - 'sainsc': Placeholder for another clustering method.
+    transcript_id (str, optional): Column name for the transcript IDs.
+    copy (bool): If True, returns a copy of the clustering results. If False, updates `sdata` in-place.
 
     Returns:
     Optional[anndata.AnnData]: If `copy` is True, returns an AnnData object containing the clustering results.Otherwise, updates the `sdata` object in-place and returns None.