liana.utils.expand_coordinates

liana.utils.expand_coordinates#

liana.utils.expand_coordinates(adata, sample_key, spatial_key='spatial', n_cols=None, margin=0.1)#

Lay out the spatial coordinates of multiple samples side-by-side on a grid.

Each sample is translated into its own cell of a regular grid so that samples no longer overlap in coordinate space (e.g. for joint plotting). Within a sample the transformation is a pure translation, so relative distances are preserved. The original coordinates are stored in obsm[f'{spatial_key}_original'].

Parameters:

  • adata (AnnData) – Annotated data object with spatial coordinates in obsm[spatial_key].

  • sample_key (str) – Column in adata.obs identifying the sample each observation belongs to.

  • spatial_key (str (default: 'spatial')) – Key in adata.obsm holding the (n_obs, 2) coordinate matrix.

  • n_cols (int | None (default: None)) – Number of columns in the grid. Defaults to a roughly square layout.

  • margin (float (default: 0.1)) – Fractional spacing between grid cells, relative to the largest sample extent. margin=0 packs cells edge-to-edge.

Return type:

AnnData

Returns:

A copy of adata with expanded coordinates in obsm[spatial_key] and the original coordinates preserved in obsm[f'{spatial_key}_original'].