omicverse.pl.calculate_gene_density

omicverse.pl.calculate_gene_density#

omicverse.pl.calculate_gene_density(adata, features, basis='X_umap', dims=(0, 1), adjust=1, min_expr=0.1, layer=None, use_raw=None)[源代码]#

Calculate weighted kernel density estimates for gene expression on 2D embeddings.

Computes KDE for each feature using expression values as weights and stores density values in adata.obs as ‘density_{feature}’ columns.

参数:

  • adata – Annotated data object with embedding coordinates

  • features – List of gene names or feature names to process

  • basis (default: 'X_umap') – Key in adata.obsm containing 2D embedding coordinates (‘X_umap’)

  • dims (default: (0, 1)) – Embedding dimensions to use as (x_dim, y_dim) ((0, 1))

  • adjust (default: 1) – Bandwidth scaling factor for KDE (1)

  • min_expr (default: 0.1) – Minimum expression threshold for including cells (0.1)

  • layer (default: None) – Read expression from adata.layers[layer] instead of .X (None)

  • use_raw (default: None) – Force (True) or forbid (False) reading from adata.raw. None reads .X and falls back to .raw only for names that are absent from .var_names — see ov.pl.get_values (None)

返回:

Updates adata.obs with density_{feature} columns

返回类型:

None

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