liana.method.genericMistyData¶
- liana.method.genericMistyData(intra, intra_use_raw=False, intra_layer=None, extra=None, extra_use_raw=False, extra_layer=None, nz_threshold=0.1, add_para=True, spatial_key='spatial', set_diag=False, kernel='misty_rbf', bandwidth=100, zoi=0, cutoff=0.1, add_juxta=True, n_neighs=6, max_neighs=18, verbose=False)¶
Construct a MistyData object from an AnnData object with views as presented in the manuscript.
- Parameters:
- intraanndata.AnnData
AnnData object with the intraview
- intra_use_rawbool, optional (default: False)
Whether to use the raw data of the intraview.
- intra_layerstr, optional (default: None)
The layer of the intraview to use.
- extraanndata.AnnData, optional (default: None)
AnnData object with the extraview(s). If None, the extraview is set to be the same as the intraview.
- extra_use_rawbool, optional (default: False)
Whether to use the raw data of the extraview.
- extra_layerstr, optional (default: None)
The layer of the extraview(s) to use.
- nz_threshold: `float`, optional (default: 0.1)
The threshold for the number of non-zero entries in each view.
- add_parabool, optional (default: True)
Whether to add the paraview.
- spatial_keystr, optional (default: ‘spatial’)
The key in adata.obsm where the spatial coordinates are stored.
- set_diagbool, optional (default: True)
Whether to set the diagonal of the connectivity matrix to 1.
- kernelstr, optional (default: ‘misty_rbf’)
A radial basis function kernel to use for the generation of the connectivity matrix for the paraview. Default is ‘misty_rbf’, a kernel derivative of a Gaussian kernel.
- bandwidthfloat, optional (default: 100)
The bandwidth of the kernel.
- zoifloat, optional (default: 0)
The zone of indifference of the kernel, i.e. the kernel is set to 0 for distances smaller than zoi.
- cutofffloat, optional (default: 0.1)
The cutoff for the connectivity matrix.
- add_juxtabool, optional (default: True)
Whether to add the juxtaview. The juxtaview is constructed using only the nearest neighbors. A bandwidth of 5 times the bandwidth of the paraview is used to ensure that the nearest neighbors within the radius.
- n_neighsint, optional (default: 6)
The number of neighbors to consider when constructing the juxtaview.
- max_neighs: `int`, optional (default: 18)
The maximum number of neighbors to consider when constructing the Paraview.
- verbosebool, optional (default: False)
Whether to print progress.
- Returns:
- MistyData object with the intra view, and two fixed extra view(s): para and juxta.