scglue.genomics.rna_anchored_guidance_graph

scglue.genomics.rna_anchored_guidance_graph(rna, *others, gene_region='combined', promoter_len=2000, extend_range=0, extend_fn=dist_power_decay, signs=None, propagate_highly_variable=True, corrupt_rate=0.0, random_state=None)[源代码]

Build guidance graph anchored on RNA genes

参数:

  • rna (AnnData) – Anchor RNA dataset

  • *others (AnnData) – Other datasets

  • gene_region (str) – Defines the genomic region of genes, must be one of {"gene_body", "promoter", "combined"}.

  • promoter_len (int) – Defines the length of gene promoters (bp upstream of TSS)

  • extend_range (int) – Maximal extend distance beyond gene regions

  • extend_fn (typing.Callable[[int], float]) – Distance-decreasing weight function for the extended regions (by default dist_power_decay())

  • signs (typing.Optional[typing.List[int]]) – Sign of edges between RNA genes and features in each *others dataset, must have the same length as *others. Signs must be one of {-1, 1}. By default, all edges have positive signs of 1.

  • propagate_highly_variable (bool) – Whether to propagate highly variable genes to other datasets, datasets in *others would be modified in place.

  • corrupt_rate (float) – CAUTION: DO NOT USE, only for evaluation purpose

  • random_state (typing.Union[RandomState, int, None]) – CAUTION: DO NOT USE, only for evaluation purpose

返回类型:

MultiDiGraph

返回:

graph – Prior regulatory graph

备注

In this function, features in the same dataset can only connect to anchor genes via the same edge sign. For more flexibility, please construct the guidance graph manually.