This repository contains code for data analysis and figures reported in the manuscript "ClustSIGNAL identifies cell types and subtypes using an adaptive smoothing approach for scalable spatial clustering".
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Simulation analysis - see Simulation_scripts folder.
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Simulated_dataAnalysis: simulated data generation, parameter testing, benchmarking adaptive smoothing, stress testing - sparsity and segmentation errors, assessing clustering stability.
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simulation_functions: functions supporting simulation analysis.
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Benchmarking analysis - see Benchmarking_scripts folder.
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Benchmarking_dataAnalysis: benchmarking runs 4 methods (ClustSIGNAL, BANKSY, BASS, SpatialPCA) on 4 real-world datasets (SeqFISH mouse embryo, Xenium breast cancer, CosMx lung cancer, MERFISH mouse hypothalamus).
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benchmarking_functions: wrapper functions for methods.
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Main figures - see Figures folder.
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Fig2_ simulations: simulation figure panels.
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Fig3_benchmarking: benchmarking figure panels.
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Fig4_dataAnalysis: data analysis figure panels, and related analyses.
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Supplementary materials - see Supplementary folder.
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Suppl_analysis: entropy analysis.
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Suppl_figs: supplementary figures.
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