liana.method.genericMistyData

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:

  • intra (AnnData) – AnnData object with the intraview

  • intra_use_raw (bool (default: False)) – Whether to use the raw data of the intraview.

  • intra_layer (str (default: None)) – The layer of the intraview to use.

  • extra (AnnData (default: None)) – AnnData object with the extraview(s). If None, the extraview is set to be the same as the intraview.

  • extra_use_raw (bool (default: False)) – Whether to use the raw data of the extraview.

  • extra_layer (str (default: None)) – The layer of the extraview(s) to use.

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

  • add_para (bool (default: True)) – Whether to add the paraview.

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

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

  • kernel (str (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.

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

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

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

  • add_juxta (bool (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_neighs (int (default: 6)) – The number of neighbors to consider when constructing the juxtaview.

  • max_neighs (int (default: 18)) – The maximum number of neighbors to consider when constructing the Paraview.

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

Return type:

MistyData

Returns:

MistyData object with the intra view, and two fixed extra view(s): para and juxta.