spaflow 0.1.0__tar.gz

spaflow-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 huchen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

spaflow-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: spaflow
+Version: 0.1.0
+Summary: A spatial CCC tool to infer ligand-receptor interaction
+Keywords: anndata,bioinformatics,ligand-receptor,scanpy,spatial-transcriptomics,squidpy
+Author: huchen
+Author-email: huchen <chen.13589@osu.edu>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: scanpy[leiden]>=1.10.3
+Requires-Dist: squidpy>=1.6.1
+Requires-Dist: setuptools<82
+Requires-Dist: upsetplot==0.9.0
+Requires-Dist: adjusttext==1.3.0
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+# spaflow
+
+`spaflow` is a spatial cell-cell communication tool for ligand-receptor interaction analysis in spatial transcriptomics data.
+
+It is designed to answer a practical question:
+
+"Where are ligand-receptor signals active in tissue, and which locations show stronger-than-expected spatial communication?"
+
+The package is built around `Scanpy` and `Squidpy` and uses spatial permutation testing to identify ligand-receptor hotspots.
+
+## Installation
+
+Create the envionment and install from PyPI:
+
+```bash
+conda create -n spaflow python=3.10 -y
+pip install spaflow
+```
+
+If you are working from the repository:
+
+```bash
+uv sync
+```
+
+## Tutorial
+
+The main tutorial lives in [tutorial.ipynb](tutorial.ipynb). The workflow is:
+
+1. Load a spatial `AnnData` object.
+2. Filter the ligand-receptor database to pairs supported by the dataset.
+3. Run `spaflow`.
+4. Visualize ligand-receptor activity and hotspot calls.
+
+### 1. Load data
+
+```python
+import warnings
+
+warnings.filterwarnings("ignore")
+
+import scanpy as sc
+from spaflow import filter_lr_database, run_spaflow
+
+adata = sc.read("your_data.h5ad")
+```
+
+### 2. Filter the ligand-receptor database
+
+```python
+df_ligrec = filter_lr_database(adata)
+df_ligrec.head()
+```
+
+By default, this keeps supported ligand-receptor pairs for secreted signaling.
+
+### 3. Run SpaFlow
+
+```python
+spaflow_adata = run_spaflow(adata, df_ligrec)
+```
+
+### 4. Visualize results
+
+The tutorial notebook shows a spatial plot for `TNFSF14-LTBR`:
+
+```python
+lr = "TNFSF14-LTBR"
+
+spaflow_adata.uns[f"{lr}_sig_colors"] = ["#DDDDDD", "#EE6677"]
+
+sc.pl.spatial(
+    spaflow_adata,
+    color=[lr, f"{lr}_sig", "Classes"],
+    img_key=None,
+    size=1.5,
+    frameon=False,
+    cmap="Spectral_r",
+)
+```
+
+In this example, `"Classes"` is an annotation column already present in the tutorial dataset. Replace it with a column from your own `adata.obs` if needed.
+
+## Output
+
+`run_spaflow` returns a copy of the input `AnnData` with additional columns in `adata.obs`.
+
+For each ligand-receptor complex, the output typically includes:
+
+- `<complex>`: ligand-receptor interaction activity
+- `<complex>_sig`: ligand-receptor interaction hotspots
+
+
+These outputs can be used directly in `scanpy.pl.spatial` or downstream statistical summaries.
+
+
+
+## Notes
+- The notebooks under `figures/` are manuscript-oriented analysis notebooks rather than package onboarding material.

spaflow-0.1.0/README.md

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+# spaflow
+
+`spaflow` is a spatial cell-cell communication tool for ligand-receptor interaction analysis in spatial transcriptomics data.
+
+It is designed to answer a practical question:
+
+"Where are ligand-receptor signals active in tissue, and which locations show stronger-than-expected spatial communication?"
+
+The package is built around `Scanpy` and `Squidpy` and uses spatial permutation testing to identify ligand-receptor hotspots.
+
+## Installation
+
+Create the envionment and install from PyPI:
+
+```bash
+conda create -n spaflow python=3.10 -y
+pip install spaflow
+```
+
+If you are working from the repository:
+
+```bash
+uv sync
+```
+
+## Tutorial
+
+The main tutorial lives in [tutorial.ipynb](tutorial.ipynb). The workflow is:
+
+1. Load a spatial `AnnData` object.
+2. Filter the ligand-receptor database to pairs supported by the dataset.
+3. Run `spaflow`.
+4. Visualize ligand-receptor activity and hotspot calls.
+
+### 1. Load data
+
+```python
+import warnings
+
+warnings.filterwarnings("ignore")
+
+import scanpy as sc
+from spaflow import filter_lr_database, run_spaflow
+
+adata = sc.read("your_data.h5ad")
+```
+
+### 2. Filter the ligand-receptor database
+
+```python
+df_ligrec = filter_lr_database(adata)
+df_ligrec.head()
+```
+
+By default, this keeps supported ligand-receptor pairs for secreted signaling.
+
+### 3. Run SpaFlow
+
+```python
+spaflow_adata = run_spaflow(adata, df_ligrec)
+```
+
+### 4. Visualize results
+
+The tutorial notebook shows a spatial plot for `TNFSF14-LTBR`:
+
+```python
+lr = "TNFSF14-LTBR"
+
+spaflow_adata.uns[f"{lr}_sig_colors"] = ["#DDDDDD", "#EE6677"]
+
+sc.pl.spatial(
+    spaflow_adata,
+    color=[lr, f"{lr}_sig", "Classes"],
+    img_key=None,
+    size=1.5,
+    frameon=False,
+    cmap="Spectral_r",
+)
+```
+
+In this example, `"Classes"` is an annotation column already present in the tutorial dataset. Replace it with a column from your own `adata.obs` if needed.
+
+## Output
+
+`run_spaflow` returns a copy of the input `AnnData` with additional columns in `adata.obs`.
+
+For each ligand-receptor complex, the output typically includes:
+
+- `<complex>`: ligand-receptor interaction activity
+- `<complex>_sig`: ligand-receptor interaction hotspots
+
+
+These outputs can be used directly in `scanpy.pl.spatial` or downstream statistical summaries.
+
+
+
+## Notes
+- The notebooks under `figures/` are manuscript-oriented analysis notebooks rather than package onboarding material.

spaflow-0.1.0/pyproject.toml

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+[project]
+name = "spaflow"
+version = "0.1.0"
+description = "A spatial CCC tool to infer ligand-receptor interaction"
+readme = "README.md"
+requires-python = ">=3.10"
+license = "MIT"
+license-files = ["LICENSE"]
+authors = [
+    { name = "huchen", email = "chen.13589@osu.edu" }
+]
+keywords = [
+    "anndata",
+    "bioinformatics",
+    "ligand-receptor",
+    "scanpy",
+    "spatial-transcriptomics",
+    "squidpy",
+]
+classifiers = [
+    "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "scanpy[leiden]>=1.10.3",
+    "squidpy>=1.6.1",
+    "setuptools<82",
+    "upsetplot==0.9.0",
+    "adjustText==1.3.0"
+
+]
+
+[dependency-groups]
+dev = [
+    "ipykernel",
+    "ipywidgets",
+]
+
+[build-system]
+requires = ["uv_build>=0.11.3,<0.12.0"]
+build-backend = "uv_build"