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:
- adataanndata.AnnData
AnnData object
- resource_namestr, optional (default: ‘consensus’)
The name of the resource to use. See show_resources for available resources.
- resourcepandas.DataFrame, optional (default: None)
A resource in the form of a pandas DataFrame. If None, the resource is selected using select_resource.
- nz_thresholdfloat, optional (default: 0.1)
The threshold for the number of non-zero entries in each view.
- use_rawbool, optional (default: False)
Whether to use the raw data of the AnnData object.
- layerstr, optional (default: None)
The layer of the AnnData object to use.
- spatial_keystr, optional (default: ‘spatial’)
The key in adata.obsm where the spatial coordinates are stored.
- kernelstr, optional (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.
- bandwidthfloat, optional (default: 100)
The bandwidth of the kernel.
- set_diagbool, optional (default: True)
Whether to set the diagonal of the connectivity matrix to 1.
- cutofffloat, optional (default: 0.1)
The minimum value cutoff for the connectivity matrix.
- zoifloat, optional (default: 0)
Zone of indifference of the kernel, i.e. the kernel is set to 0 for distances smaller than zoi.
- verbosebool, optional (default: False)
Whether to print progress.
- Returns:
- A MistyData object with receptors in the intra view & ligands in the extra view.