multivelo.set_velocity_genes

multivelo.set_velocity_genes(adata, likelihood_lower=0.05, rescale_u_upper=None, rescale_u_lower=None, rescale_c_upper=None, rescale_c_lower=None, primed_upper=None, primed_lower=None, decoupled_upper=None, decoupled_lower=None, alpha_c_upper=None, alpha_c_lower=None, alpha_upper=None, alpha_lower=None, beta_upper=None, beta_lower=None, gamma_upper=None, gamma_lower=None, scale_cc_upper=None, scale_cc_lower=None)

Reset velocity genes.

This function resets velocity genes based on criteria of variables.

Parameters:

  • adata (AnnData) – Anndata result from dynamics recovery.

  • likelihood_lower (float (default: 0.05)) – Minimum ikelihood.

  • rescale_u_upper (float (default: None)) – Maximum rescale_u.

  • rescale_u_lower (float (default: None)) – Minimum rescale_u.

  • rescale_c_upper (float (default: None)) – Maximum rescale_c.

  • rescale_c_lower (float (default: None)) – Minimum rescale_c.

  • primed_upper (float (default: None)) – Maximum primed interval.

  • primed_lower (float (default: None)) – Minimum primed interval.

  • decoupled_upper (float (default: None)) – Maximum decoupled interval.

  • decoupled_lower (float (default: None)) – Minimum decoupled interval.

  • alpha_c_upper (float (default: None)) – Maximum alpha_c.

  • alpha_c_lower (float (default: None)) – Minimum alpha_c.

  • alpha_upper (float (default: None)) – Maximum alpha.

  • alpha_lower (float (default: None)) – Minimum alpha.

  • beta_upper (float (default: None)) – Maximum beta.

  • beta_lower (float (default: None)) – Minimum beta.

  • gamma_upper (float (default: None)) – Maximum gamma.

  • gamma_lower (float (default: None)) – Minimum gamma.

  • scale_cc_upper (float (default: None)) – Maximum scale_cc.

  • scale_cc_lower (float (default: None)) – Minimum scale_cc.

Returns:

velo_s_genes, velo_u_genes, velo_chrom_genes (.var) – new velocity genes for each modalities.