spatial_feature¶

Purpose¶

Extracts mutation-level spatial consistency and neighborhood-distribution features from spot genotypes.

Upstream¶

• genotyping

Required inputs¶

• ind_geno_filter_mutation_list
• spot_geno_file
• tissue_position

Input interpretation¶

Input key	Source	Required	Interpretation
ind_geno_filter_mutation_list	genotyping output	Yes	Candidate mutation list used to iterate spatial-feature extraction targets.
spot_geno_file	genotyping output	Yes	Spot-level genotype/probability table for spatial consistency tests.
tissue_position	input details	Yes (Visium)	Spot coordinate matrix required for neighborhood and directional spatial metrics.

Parameters¶

From steps.spatial_feature:

• alpha
• thr_r2
• thr_prob
• thr_likelihood
• thr_vaf
• plot_supp
• fig_size
• method
• num_directions

Parameter interpretation highlights¶

Parameter	Interpretation
alpha	Significance threshold used in statistical spatial tests.
thr_r2, thr_prob, thr_likelihood, thr_vaf	Core cutoffs that define mutation-spatial consistency criteria.
method	Spatial modeling method (for example LDA-style directional aggregation).
num_directions	Direction granularity for directional spatial summaries.
plot_supp, fig_size	Controls supplementary plotting behavior and figure size.

Outputs¶

• spatial_feature: output_dir/spatial_feature/spatial_feature.txt
• parquet mirror: spatial_feature.parquet

Tuning notes¶

• This step is parallelized across mutation identifiers.
• Spatial metrics include distribution tests and VAF consistency summaries.