opendvp.tl.filter_by_annotation

opendvp.tl.filter_by_annotation(adata, path_to_geojson, cell_id_col='CellID', x_y=('X_centroid', 'Y_centroid'), any_label='ANY')

Filter cells by annotation in a geojson file using spatial indexing.

This function assigns annotation classes to cells in an AnnData object by spatially joining cell centroids with polygons from a GeoJSON file. Each annotation class becomes a boolean column in adata.obs.

Return type:

AnnData

Parameters:

adataad.AnnData

AnnData object with cell centroids in adata.obs[['X_centroid', 'Y_centroid']] and unique ‘CellID’.

path_to_geojsonstr

Path to the GeoJSON file containing polygon annotations with a ‘classification’ property.

cell_id_colstr, default ‘CellID’

Name of the column in adata.obs that uniquely identifies each cell.

x_ySequence[str], default (“X_centroid”, “Y_centroid”)

Names of columns in adata.obs containing the X and Y spatial coordinates of cells.

any_labelstr, default ‘ANY’

Name for the column indicating if a cell is inside any annotation. This is to be used for naming the group of annotations, for example: If pathologist annotated tissue regions, call this: ‘tissue_ann’ If microscopist annotated imaging artefacts, call this: ‘img_arts’

Returns:

ad.AnnData

The input AnnData with new boolean columns in .obs for each annotation class and a summary column.

Raises:

ValueError

If the GeoJSON is missing geometry, not polygons, or if required columns are missing.