liana.method.lrMistyData

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liana.method.lrMistyData#

liana.method.lrMistyData(adata, resource_name='consensus', resource=None, nz_threshold=0.1, use_raw=False, layer=None, spatial_key='spatial', kernel='misty_rbf', bandwidth=100, set_diag=False, cutoff=0.1, zoi=0, verbose=False)#

Generate a MistyData object from an AnnData object in ligand-receptor format.

Parameters:

  • adata (AnnData) – AnnData object

  • resource_name (str (default: 'consensus')) – The name of the resource to use. See show_resources for available resources.

  • resource (DataFrame (default: None)) – A resource in the form of a pandas DataFrame. If None, the resource is selected using select_resource.

  • nz_threshold (float (default: 0.1)) – The threshold for the number of non-zero entries in each view.

  • use_raw (bool (default: False)) – Whether to use the raw data of the AnnData object.

  • layer (str (default: None)) – The layer of the AnnData object to use.

  • spatial_key (str (default: 'spatial')) – The key in adata.obsm where the spatial coordinates are stored.

  • kernel (str (default: 'misty_rbf')) – A radial basis function kernel to use for the generation of the connectivity matrix for the extra view. Default is ‘misty_rbf’, a kernel derivative of a Gaussian kernel.

  • bandwidth (float (default: 100)) – The bandwidth of the kernel.

  • set_diag (bool (default: False)) – Whether to set the diagonal of the connectivity matrix to 1.

  • cutoff (float (default: 0.1)) – The minimum value cutoff for the connectivity matrix.

  • zoi (float (default: 0)) – Zone of indifference of the kernel, i.e. the kernel is set to 0 for distances smaller than zoi.

  • verbose (bool (default: False)) – Whether to print progress.

Return type:

MistyData

Returns:

A MistyData object with receptors in the intra view & ligands in the extra view.

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