visualization

Bundle of general-purpose diagnostic plots. Given the cell-level AnnData and the sample-level pseudobulk, it can emit three categories of figure (each individually toggleable):

1. Cell-type dendrogram — hierarchical clustering of cell types based on their pseudobulk expression profiles.
2. Cell-type proportion PCA — PCA of per-sample cell-type proportions with samples colored by a user-specified grouping column.
3. Cell-type expression UMAP — UMAP of samples on the pseudobulk expression embedding.

Supply one or more grouping_columns (and optionally age_bin_size for age-based faceting) to control how samples are colored.

Source: visualization/visualization_other.py:73

Signature

def visualization(
    AnnData_cell,
    pseudobulk_anndata,
    output_dir,
    grouping_columns=None,
    age_bin_size=None,
    age_column="age",
    verbose=True,
    plot_dendrogram_flag=True,
    plot_cell_type_proportions_pca_flag=False,
    plot_cell_type_expression_umap_flag=False,
)

Parameters

Name	Type	Default	Description
AnnData_cell	AnnData	—	Cell-level AnnData carrying the cell-type labels.
pseudobulk_anndata	AnnData	—	Sample-level pseudobulk with DR in .obsm.
output_dir	str	—	Writes plots under a grouping-aware subdirectory of {output_dir}/visualization/.
grouping_columns	list, optional	None	.obs columns used for sample coloring. Required for proportion PCA / expression UMAP plots.
age_bin_size	int, optional	None	Optional age bin width; enables age-as-category coloring.
age_column	str	"age"	Column holding sample age.
verbose	bool	True	Print progress.
plot_dendrogram_flag	bool	True	Emit the cell-type dendrogram PNG.
plot_cell_type_proportions_pca_flag	bool	False	Emit proportion PCAs per grouping column.
plot_cell_type_expression_umap_flag	bool	False	Emit expression UMAPs per grouping column.

Returns

None. Side effects only.

Output files

Under {output_dir}/visualization/:

• cell_type_dendrogram.png
• proportion_pca_{grouping_column}.png (per flag)
• expression_umap_{grouping_column}.png (per flag)

Usage

from sampledisco.visualization.visualization_other import visualization

visualization(
    AnnData_cell=adata_cell,
    pseudobulk_anndata=pseudo_adata,
    output_dir="sampledisco_demo_output/rna",
    grouping_columns=["sev.level"],
    plot_dendrogram_flag=True,
    plot_cell_type_proportions_pca_flag=True,
    plot_cell_type_expression_umap_flag=False,
)