SpatialQuery 0.0.4__tar.gz → 0.0.5__tar.gz

{spatialquery-0.0.4/SpatialQuery.egg-info → spatialquery-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SpatialQuery
-Version: 0.0.4
+Version: 0.0.5
 Summary: Spatial query tools for analyzing spatial transcriptomics data
 Author-email: Shaokun An <shan12@bwh.harvard.edu>
 License-Expression: MIT
@@ -62,6 +62,15 @@ pip install SpatialQuery
 
 Full documentation, tutorials, and API reference: **[https://spatialquery.readthedocs.io/en/latest/](https://spatialquery.readthedocs.io/en/latest/)**
 
+## Reproducibility
+
+The following tutorials reproduce the main analyses presented in our manuscript:
+
+- [Mouse organogenesis — single-FOV analysis (seqFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_1.html)
+- [Kidney disease atlas — multi-condition analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_2.html)
+- [Colorectal cancer microenvironment — spatial proteomics (CODEX)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_3.html)
+- [Whole-brain atlas — large-scale analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_4.html)
+
 ## Quick Start
 
 ```python

{spatialquery-0.0.4 → spatialquery-0.0.5}/README.md

@@ -25,6 +25,15 @@ pip install SpatialQuery
 
 Full documentation, tutorials, and API reference: **[https://spatialquery.readthedocs.io/en/latest/](https://spatialquery.readthedocs.io/en/latest/)**
 
+## Reproducibility
+
+The following tutorials reproduce the main analyses presented in our manuscript:
+
+- [Mouse organogenesis — single-FOV analysis (seqFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_1.html)
+- [Kidney disease atlas — multi-condition analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_2.html)
+- [Colorectal cancer microenvironment — spatial proteomics (CODEX)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_3.html)
+- [Whole-brain atlas — large-scale analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_4.html)
+
 ## Quick Start
 
 ```python

{spatialquery-0.0.4 → spatialquery-0.0.5}/SpatialQuery/spatial_query.py

@@ -1536,6 +1536,7 @@ def interactive_motif(
     sp,
     zarr_path: str,
     spatialSpotRadius: float = 1,
+    use_adata_store: bool = False,
 ):
     """
     Create an interactive Vitessce widget to explore spatial motifs.
@@ -1558,6 +1559,9 @@ def interactive_motif(
     spatialSpotRadius : float, default=1
         Radius for spatial spots in the Vitessce visualization. Adjust based
         on data density and spatial coordinate scale.
+    use_adata_store : bool, default=False
+        If True, pass the zarr path via ``adata_store`` (for HubMAP workspace).
+        If False, pass via ``adata_path`` (for local usage).
 
     Returns
     -------
@@ -1638,8 +1642,9 @@ def interactive_motif(
 
     vc = VitessceConfig(schema_version="1.0.16", name="SpatialQuery")
 
+    _adata_key = "adata_store" if use_adata_store else "adata_path"
     wrapper_kwargs = dict(
-        adata_path=zarr_path,
+        **{_adata_key: zarr_path},
         obs_set_paths=[f"obs/{label_key}"],
         obs_set_names=["Cell Type"],
         obs_spots_path=f"obsm/{spatial_key}",
@@ -1652,7 +1657,6 @@ def interactive_motif(
     dataset = vc.add_dataset("Query results").add_object(AnnDataWrapper(**wrapper_kwargs))
 
     spatial_view = vc.add_view("spatialBeta", dataset=dataset)
-    lc_view = vc.add_view("layerControllerBeta", dataset=dataset)
     sets_view = vc.add_view("obsSets", dataset=dataset)
     sq_view = vc.add_view("spatialQuery", dataset=dataset)
     sq_heatmap_view = vc.add_view("spatialQueryHeatmap", dataset=dataset)
@@ -1661,7 +1665,7 @@ def interactive_motif(
         ["Cell Type", ct] for ct in sp.labels.unique().tolist()
     ]
 
-    linked_views = [spatial_view, lc_view, sets_view, sq_view]
+    linked_views = [spatial_view, sets_view, sq_view]
     if has_expression:
         features_view = vc.add_view("featureList", dataset=dataset)
         linked_views.append(features_view)
@@ -1672,21 +1676,21 @@ def interactive_motif(
         [plugin.additional_obs_sets, plugin.obs_set_color, initial_obs_set_selection, "cellSetSelection"],
     )
 
-    vc.link_views_by_dict([spatial_view, lc_view], {
+    vc.link_views_by_dict([spatial_view], {
         "spotLayer": CL([{"obsType": "cell", "spatialSpotRadius": spatialSpotRadius}]),
     })
 
     if has_expression:
         vc.layout(
             vconcat(
-                hconcat(spatial_view, vconcat(lc_view, features_view)),
+                hconcat(spatial_view, features_view, split=[2, 1]),
                 hconcat(sets_view, sq_heatmap_view, sq_view),
             )
         )
     else:
         vc.layout(
             vconcat(
-                hconcat(spatial_view, lc_view),
+                spatial_view,
                 hconcat(sets_view, sq_heatmap_view, sq_view),
             )
         )

{spatialquery-0.0.4 → spatialquery-0.0.5/SpatialQuery.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SpatialQuery
-Version: 0.0.4
+Version: 0.0.5
 Summary: Spatial query tools for analyzing spatial transcriptomics data
 Author-email: Shaokun An <shan12@bwh.harvard.edu>
 License-Expression: MIT
@@ -62,6 +62,15 @@ pip install SpatialQuery
 
 Full documentation, tutorials, and API reference: **[https://spatialquery.readthedocs.io/en/latest/](https://spatialquery.readthedocs.io/en/latest/)**
 
+## Reproducibility
+
+The following tutorials reproduce the main analyses presented in our manuscript:
+
+- [Mouse organogenesis — single-FOV analysis (seqFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_1.html)
+- [Kidney disease atlas — multi-condition analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_2.html)
+- [Colorectal cancer microenvironment — spatial proteomics (CODEX)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_3.html)
+- [Whole-brain atlas — large-scale analysis (MERFISH)](https://spatialquery.readthedocs.io/en/latest/tutorials/tutorial_4.html)
+
 ## Quick Start
 
 ```python

{spatialquery-0.0.4 → spatialquery-0.0.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "SpatialQuery"
-version = "0.0.4"
+version = "0.0.5"
 description = "Spatial query tools for analyzing spatial transcriptomics data"
 readme = "README.md"
 license = "MIT"