GitHub - BiocPy/SpatialFeatureExperiment

A Python package for storing and analyzing spatial-omics experimental data. This package provide the SpatialFeatureExperiment class, based on the R package and class.

Install

To get started, install the package from PyPI

pip install spatialfeatureexperiment

Quick Usage

This package uses shapely and geopandas to support the *_geometries slots.

from spatialexperiment import SpatialFeatureExperiment
import numpy as np
import geopandas as gpd
from shapely.geometry import Polygon

nrows = 200
ncols = 500
counts = np.random.rand(nrows, ncols)
polys = gpd.GeoSeries(
    [
        Polygon([(1, -1), (1, 0), (0, 0)]),
        Polygon([(3, -1), (4, 0), (3, 1)]),
    ]
)

colgeoms = {"polygons" : gpd.GeoDataFrame({"geometry": polys})}
tspe = SpatialFeatureExperiment(assays={"spots": counts}, col_geometries=colgeoms)

Note

This project has been set up using BiocSetup and PyScaffold.