tomas.infer.heteroDbl_bc

tomas.infer.heteroDbl_bc(adata, dbl, d_groupby, ct_groupby, g2meta=None, de_sorted=None, mg_gnum=[10, 10], threshold=None, threshold_x=None, threshold_y=None, vis=True, log=True, return_fig=False, dpi=80)

Identification and refinement of a certain type of heterotypic doublets specified by “dbl”.

Parameters:

  • adata (AnnData) – UMI matrix of all droplet population.

  • dbl (str) – Heterotypic dboulet group to be investigated, named by two cell types linked by ‘_’.

  • d_groupby (str) – The key of the droplet annotation (‘Homotypic’ or ‘Heterotypic’) results stored in adata.obs.

  • ct_groupby (str) – The key of the cell type annotation results stored in adata.obs.

  • g2meta (list, optional) – A list of genes. The default is None.

  • de_sorted (data frame, optional) – Output of function ‘extract_specific_genes’. The default is None.

  • mg_gnum (list, optional) – Number of DEG merged to identify heterodbls. The default is [10,10].

  • threshold (list, optional) – Cutoff of expression levels in current cell type pair to identify heterodbls. The default is None.

  • threshold_x (float, optional) – Cutoff of expression level in current (x axis) cell type to identify heterodbls. The default is None.

  • threshold_y (float, optional) – Cutoff of expression level in current (y axis) cell type to identify heterodbls. The default is None.

  • vis (bool, optional) – Whether to visualize the heterodlb identification results. The default is True.

  • log (bool, optional) – Whether to calculate in logarithmic form. The default is True (recommended).

  • return_fig (bool, optional) – Whether to return the figure object. The default is False.

Raises:

ValueError – Inspect if genes to be merged for heterotypic doublet detection are specified in a proper way.

Returns:

Idnetified heterotypic doublets composed by input cell type pair.

Return type:

list