Package index • SpaPheno

Example data

data for SpaPheno

osmFISH_bulk_coordinate: Spatial Coordinates for Simulated Bulk Samples (osmFISH)

osmFISH_bulk_decon: Simulated Pseudo-Bulk Deconvolved Cell Type Compositions (osmFISH)

osmFISH_bulk_pheno: Simulated Phenotypic Labels for Pseudo-Bulk Samples (osmFISH)

osmFISH_metadata_cellType: Simulated Cell Type Labels for osmFISH Dataset

osmFISH_metadata_region: Simulated Region Labels for osmFISH Dataset

osmFISH_phenotype_simu: Simulated Phenotype Labels for osmFISH Dataset

Data Analysis

Functions for Data Analysis

BuildPhenoModelAutoAlpha(): Build Elastic Net Model with Automatic Alpha Selection

Cell_type_neighborhood(): Compute Local Cell Type Composition in the Spatial Neighborhood

compute_shap_spatial(): Compute SHAP Values for Spatial Transcriptomics Data

FeatureImportanceCoef(): Plot Feature Coefficients from a glmnet Model

generate_simulated_bulk_data(): Generate Simulated Pseudo-Bulk Data for Two Phenotypes

GeneratePermutations(): Generate Permutation Scores for Model Significance Testing

PhenoAbundancePlot(): Visualize Average Cell Type Abundance by Phenotype Label

PhenotypeHclust(): Phenotype-based Hierarchical Clustering and Visualization of Cell Type Distributions

PhenotypePlot(): Plot Spatial Phenotype Significance Map with Permutation Thresholds

Precision_Recall_macroF1(): Compute Macro-Averaged Precision, Recall, and F1 Score for Multiclass Classification

SpatialKNN(): Compute K-Nearest Neighbors for Spatial Coordinates

SpatialPhenoMap(): Map Bulk Phenotype to Spatial Transcriptomics via Interpretable Modeling

STplot(): Spatial Transcriptomics Scatter Plot with Labels

ThresholdPlot(): Plot Prediction vs. Permutation Distributions with Significance Thresholds

SHAP in interpretability

Functions for Interpretable Model

SpaPheno_SHAP_dependence_plot(): SHAP Dependence Plot for Selected Features

SpaPheno_SHAP_residual_analysis(): Residual-based SHAP Analysis and Visualization in Spatial Transcriptomics

SpaPheno_SHAP_summary_plot(): SHAP Summary Plot

SpaPheno_SHAP_waterfall_plot(): SHAP Waterfall Plot for a Single Sample