liana.utils.interpolate_adata

liana.utils.interpolate_adata#

liana.utils.interpolate_adata(target, reference, spatial_key, layer=None, use_raw=True, method='linear', fill_value=0, verbose=False)#

Interpolates spatial data from a target AnnData object to a reference AnnData object based on spatial coordinates.

The function creates a new AnnData object where the .X attribute is filled with interpolated data using the specified method.

Parameters:

  • target (AnnData) – The AnnData object to be interpolated.

  • reference (AnnData) – The AnnData object to be used as reference.

  • spatial_key (str) – Key in adata.obsm that contains the spatial coordinates. Default is 'spatial'.

  • layer (str (default: None)) – Layer in anndata.AnnData.layers to use. If None, use anndata.AnnData.X.

  • use_raw (bool (default: True)) – Use raw attribute of adata if present.

  • method (str (default: 'linear')) – Interpolation method. See scipy.interpolate.griddata for more information.

  • fill_value (float (default: 0)) – Value to fill in for points outside of the convex hull of the input points.

  • verbose (bool (default: False)) – Verbosity flag.

Return type:

AnnData

Returns:

AnnData: A new AnnData object with the same metadata as the reference but with interpolated spatial data in .X.