From ce9bfb9484effe96ca37d55a0a48922b912612ce Mon Sep 17 00:00:00 2001
From: Tim Treis <tim.treis@stud.uni-heidelberg.de>
Date: Thu, 30 Jan 2025 14:50:19 -0500
Subject: [PATCH] stash
---
src/squidpy/__init__.py | 2 +-
src/squidpy/exp/__init__.py | 5 +++++
src/squidpy/exp/pl/__init__.py | 10 ++++++++++
src/squidpy/exp/pl/_spatial_qc.py | 30 ++++++++++++++++++++++++++++++
4 files changed, 46 insertions(+), 1 deletion(-)
create mode 100644 src/squidpy/exp/__init__.py
create mode 100644 src/squidpy/exp/pl/__init__.py
create mode 100644 src/squidpy/exp/pl/_spatial_qc.py
diff --git a/src/squidpy/__init__.py b/src/squidpy/__init__.py
index 5fb2b848..cfba804f 100644
--- a/src/squidpy/__init__.py
+++ b/src/squidpy/__init__.py
@@ -3,7 +3,7 @@
from importlib import metadata
from importlib.metadata import PackageMetadata
-from squidpy import datasets, gr, im, pl, read, tl
+from squidpy import datasets, exp, gr, im, pl, read, tl
try:
md: PackageMetadata = metadata.metadata(__name__)
diff --git a/src/squidpy/exp/__init__.py b/src/squidpy/exp/__init__.py
new file mode 100644
index 00000000..ef884e41
--- /dev/null
+++ b/src/squidpy/exp/__init__.py
@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from . import pl
+
+__all__ = ["pl"]
diff --git a/src/squidpy/exp/pl/__init__.py b/src/squidpy/exp/pl/__init__.py
new file mode 100644
index 00000000..c907876d
--- /dev/null
+++ b/src/squidpy/exp/pl/__init__.py
@@ -0,0 +1,10 @@
+from __future__ import annotations
+
+from squidpy.exp.pl._spatial_qc import _spatial_counts_distribution
+
+__all__ = [
+ "highly_variable_genes",
+ "normalize_pearson_residuals",
+ "normalize_pearson_residuals_pca",
+ "recipe_pearson_residuals",
+]
diff --git a/src/squidpy/exp/pl/_spatial_qc.py b/src/squidpy/exp/pl/_spatial_qc.py
new file mode 100644
index 00000000..650adba3
--- /dev/null
+++ b/src/squidpy/exp/pl/_spatial_qc.py
@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+import itertools
+import spatialdata as sd
+import spatialdata_plot
+
+_ = spatialdata_plot
+
+from squidpy._docs import d
+
+
+@d.dedent
+def _spatial_counts_distribution(
+ sdata: sd.SpatialData,
+ coordinate_system: list[str] | str | None = None,
+ sdata_plot_kwargs: dict = {},
+) -> None:
+ """
+ Plot the distribution of spatial counts.
+
+ EXPERIMENTAL: Only supports the new SpatialData interface.
+ """
+
+ if coordinate_system is not None:
+ if isinstance(coordinate_system, str):
+ coordinate_system = [coordinate_system]
+ if not all(isinstance(cs, str) for cs in coordinate_system):
+ raise ValueError("All elements in `coordinate_system` must be strings.")
+ for cs in coordinate_system:
+ pass