pyXenium.gmi.GmiModuleConfig

class GmiModuleConfig(min_abs_anchor_coefficient=0.0, min_stability_frequency=0.25, anchor_merge_correlation=0.5, expansion_correlation=0.55, expansion_spatial_lag_correlation=0.45, max_features_per_module=30, spatial_neighbor_k=4, include_spatial_features=True, write_figures=True, module_prefix='gmi_module')

Bases: object

Configuration for GMI-anchored spatial gene module discovery.

Parameters:

• min_abs_anchor_coefficient (float)

• min_stability_frequency (float)

• anchor_merge_correlation (float)

• expansion_correlation (float)

• expansion_spatial_lag_correlation (float)

• max_features_per_module (int)

• spatial_neighbor_k (int)

• include_spatial_features (bool)

• write_figures (bool)

• module_prefix (str)

__init__(min_abs_anchor_coefficient=0.0, min_stability_frequency=0.25, anchor_merge_correlation=0.5, expansion_correlation=0.55, expansion_spatial_lag_correlation=0.45, max_features_per_module=30, spatial_neighbor_k=4, include_spatial_features=True, write_figures=True, module_prefix='gmi_module')

Parameters:

• min_abs_anchor_coefficient (float)

• min_stability_frequency (float)

• anchor_merge_correlation (float)

• expansion_correlation (float)

• expansion_spatial_lag_correlation (float)

• max_features_per_module (int)

• spatial_neighbor_k (int)

• include_spatial_features (bool)

• write_figures (bool)

• module_prefix (str)

Return type:

None

Methods

__init__([min_abs_anchor_coefficient, ...])
copy_with(**updates)
to_dict()

Attributes

anchor_merge_correlation
expansion_correlation
expansion_spatial_lag_correlation
include_spatial_features
max_features_per_module
min_abs_anchor_coefficient
min_stability_frequency
module_prefix
spatial_neighbor_k
write_figures

min_abs_anchor_coefficient: float = 0.0

min_stability_frequency: float = 0.25

anchor_merge_correlation: float = 0.5

expansion_correlation: float = 0.55

expansion_spatial_lag_correlation: float = 0.45

max_features_per_module: int = 30

spatial_neighbor_k: int = 4

include_spatial_features: bool = True

write_figures: bool = True

module_prefix: str = 'gmi_module'

to_dict()

Return type:

dict[str, Any]

copy_with(**updates)

Parameters:

updates (Any)

Return type:

GmiModuleConfig