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.

fromspatialexperimentimportSpatialFeatureExperimentimportnumpyasnpimportgeopandasasgpdfromshapely.geometryimportPolygonnrows=200ncols=500counts=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.