Init spatial experiment #1

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Merged

jkanche merged 37 commits into main from init-spatial-experiment

Jan 28, 2025

.github/workflows/run-tests.yml

            
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    @@ -2,9 +2,9 @@ name: Run tests
  
    on:

      push:

        branches: [master]

        branches: [main]

      pull_request:

        branches: [master]

        branches: [main]

    jobs:

      build:

README.md

            
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    [![PyPI-Server](https://img.shields.io/pypi/v/SpatialExperiment.svg)](https://pypi.org/project/SpatialExperiment/)

    ![Unit tests](https://github.com/BiocPy/SpatialExperiment/actions/workflows/pypi-test.yml/badge.svg)

    ![Unit tests](https://github.com/BiocPy/SpatialExperiment/actions/workflows/run-tests.yml/badge.svg)

    # SpatialExperiment

    > Container class for sotring data from spatial -omics experiments

    A Python package for storing and analyzing spatial-omics experimental data. `SpatialExperiment` extends [SingleCellExperiment](https://github.com/biocpy/singlecellexperiment) with dedicated slots for image data and spatial coordinates, making it ideal for spatial transcriptomics and other spatially-resolved omics data.

    A longer description of your project goes here...

    > [!NOTE]

    >

    > This package is in **active development**.

    ## Install

    To get started, install the package from [PyPI](https://pypi.org/project/SpatialExperiment/)

    ```bash

    pip install SpatialExperiment

    pip install spatialexperiment

    ```

    ## Usage

    The `SpatialExperiment` class extends `SingleCellExperiment` with the following key attributes:

    - `spatial_coords`: A BioFrame containing spot/cell spatial coordinates relative to the image, typically including:

      - x-coordinates

      - y-coordinates

      - Additional spatial metadata

    - `img_data`: A BiocFrame containing image-related information:

      - sample_ids: Unique identifiers for each sample

      - image_ids: Unique identifiers for each image

      - data: The actual image data

      - scale_factor: Scaling factors for proper image interpretation

    - `column_data`: Contains sample_id mappings that link spots to their corresponding images

    ### Quick Start

    Here's how to create a SpatialExperiment object from scratch:

    ```python

    from spatialexperiment import SpatialExperiment, SpatialImage

    import numpy as np

    from biocframe import BiocFrame

    # Create example data

    nrows = 200  # Number of features (e.g., genes)

    ncols = 500  # Number of spots/cells

    # Generate random count data

    counts = np.random.rand(nrows, ncols)

    # Create feature annotations

    row_data = BiocFrame({

        "gene_ids": [f"gene_{i}" for i in range(nrows)],

        "gene_names": [f"Gene_{i}" for i in range(nrows)]

    })

    # Create spot/cell annotations

    col_data = BiocFrame({

        "n_genes": [50, 200] * int(ncols / 2),

        "condition": ["healthy", "tumor"] * int(ncols / 2),

        "cell_id": [f"spot_{i}" for i in range(ncols)],

        "sample_id": ["sample_1"] * int(ncols / 2) + ["sample_2"] * int(ncols / 2),

    })

    # Generate spatial coordinates

    spatial_coords = BiocFrame({

        "x": np.random.uniform(low=0.0, high=100.0, size=ncols),

        "y": np.random.uniform(low=0.0, high=100.0, size=ncols)

    })

    # Create image data

    img_data = BiocFrame({

        "sample_id": ["sample_1", "sample_1", "sample_2"],

        "image_id": ["aurora", "dice", "desert"],

        "data": [

            SpatialImage("tests/images/sample_image1.jpg"),

            SpatialImage("tests/images/sample_image2.png"),

            SpatialImage("tests/images/sample_image3.jpg"),

        ],

        "scale_factor": [1, 1, 1],

    })

    # Create SpatialExperiment object

    spe = SpatialExperiment(

        assays={"counts": counts},

        row_data=row_data,

        column_data=col_data,

        spatial_coords=spatial_coords,

        img_data=img_data,

    )

    ```

    For more detailed information about available methods and functionality, please refer to the [SingleCellExperiment documentation](https://biocpy.github.io/SingleCellExperiment/).

    <!-- biocsetup-notes -->

    ## Note

    This project has been set up using [BiocSetup](https://github.com/biocpy/biocsetup)

    and [PyScaffold](https://pyscaffold.org/).

    and [PyScaffold](https://pyscaffold.org/).

docs/conf.py

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         "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
         "setuptools": ("https://setuptools.pypa.io/en/stable/", None),
         "pyscaffold": ("https://pyscaffold.org/en/stable", None),
+        "biocframe": ("https://biocpy.github.io/BiocFrame", None),
+        "genomicranges": ("https://biocpy.github.io/GenomicRanges", None),
+        "summarizedexperiment": ("https://biocpy.github.io/SummarizedExperiment", None),
+        "biocutils": ("https://biocpy.github.io/BiocUtils", None),
+        "singlecellexperiment": ("https://biocpy.github.io/SingleCellExperiment", None),
     }
     print(f"loading configurations for {project} {version} ...", file=sys.stderr)
@@ Expand Down @@

pyproject.toml

            
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    @@ -12,14 +12,14 @@ version_scheme = "no-guess-dev"
  
    line-length = 120

    src = ["src"]

    exclude = ["tests"]

    extend-ignore = ["F821"]

    lint.extend-ignore = ["F821"]

    [tool.ruff.pydocstyle]

    [tool.ruff.lint.pydocstyle]

    convention = "google"

    [tool.ruff.format]

    docstring-code-format = true

    docstring-code-line-length = 20

    [tool.ruff.per-file-ignores]

    [tool.ruff.lint.per-file-ignores]

    "__init__.py" = ["E402", "F401"]

setup.cfg

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     # For more information, check out https://semver.org/.
     install_requires =
         importlib-metadata; python_version<"3.8"
+        pandas>=2.0
+        biocframe>=0.6
+        biocutils>=0.2
+        summarizedexperiment>=0.5
+        singlecellexperiment>=0.5.6
+        pillow>=11.0
     [options.packages.find]
@@ Expand Down @@

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