process_snapseed

hnoca.snapseed.process.process_snapseed(adata, marker_dict, ann_df, obs_key='leiden', prefix='snapseed', fill_na=True, base_colormap='tab10', get_colors=True, sample_key=None, min_abs_freq=5, min_rel_freq=0.001, rotation_step=0.05, saturation_adjust=0.2, brightness_adjust=0.1, min_hue_separation=0.05)

Map the cluster assignments of annotate_hierarchy() onto adata.obs, one column per level.

Categories follow the hierarchy depth-first; colors are derived from the parent's color, so that subtypes look like their parent across levels.

Parameters:

Name	Type	Description	Default
adata	AnnData	AnnData object.	required
marker_dict	dict	The marker hierarchy passed to annotate_hierarchy().	required
ann_df	DataFrame	The "assignments" returned by annotate_hierarchy(): one column per level (level_1, level_2, ...), indexed by cluster.	required
obs_key	str	Column in adata.obs with the cluster labels passed to annotate_hierarchy().	'leiden'
prefix	str	Prefix for the new columns, named <prefix>_level_<n>.	'snapseed'
fill_na	bool	Whether clusters without an annotation at a level keep that of the previous (coarser) level.	True
base_colormap	str	Name of a matplotlib colormap for the top-level categories.	'tab10'
get_colors	bool	Whether to write colors consistent across levels to adata.uns["<prefix>_level_<n>_colors"].	True
sample_key	str | None	Column in adata.obs with the sample. If given, per sample and level, categories below min_abs_freq cells or below a fraction min_rel_freq of the sample's annotated cells are set to missing.	None
min_abs_freq	int | None	Minimum number of cells of a category in a sample to retain it.	5
min_rel_freq	float | None	Minimum fraction of a sample's annotated cells in a category to retain it.	0.001
rotation_step	float	Step size for hue rotation when generating child colors.	0.05
saturation_adjust	float	Adjustment factor for saturation (positive to increase, negative to decrease).	0.2
brightness_adjust	float	Adjustment factor for brightness (positive to increase, negative to decrease).	0.1
min_hue_separation	float	Minimum separation between hue values of child colors.	0.05

Returns

Nothing; writes `adata.obs["<prefix>_level_<n>"]` and, with `get_colors`, their colors to `adata.uns`.