API Documents

`zoom.core` - Core Class

Main class used for quick analyses in zoom.

ZOOM: Implementation of cross-validation PLS-R and traditional imaging-transcriptomics paradigm and spatial permutation test-based GSEA.
ZOOM_SC: Calculation of single-cell enrichment scores of SBP-relevant gene sets and single-cell level statistical significance.

`zoom.core.ZOOM`(expression, SBP, SBP_perm[, ...])	The ZOOM class serves as fundation for this package.It implements a framework for partial least squares regression (PLS-R) applied to anatomically comprehensive transcriptomics and spatial brain phenotypic data.
`zoom.core.ZOOM_SC`(adata, expression, SBP, ...)	The ZOOM_SC class extends traditional imaging-transcriptomics paradigm (ZOOM class) by link SBP-relevant gene sets with single-cell RNA sequencing dataset.

`zoom.data_loader` - Data Loader

Functionality for loading single-cell RNA sequencing data, surface- based spatial brain phenotypes, parcellation and data frame.

`zoom.data_loader.load_sc`(adata, flag_sparse)	Load and check scRNA-seq file (.h5ad).
`zoom.data_loader.load_gii`(gii, atlas, ...)	Load GIFTI image.
`zoom.data_loader.load_parc`(parcellation, ...)	Load parcellation image.

`zoom.prepare` - Prepare Input Data

Functionality for perparing neccessary data for ZOOM. - Regional AHBA processing pipeline optimized for cortical samples. - Regional SBP and spatial permutation test. - scRNA-seq preprocess and calculate gene specificity scores.

`zoom.prepare.abagen_ctx`(atlas, atlas_info, ...)	AHBA processing pipeline optimized for cortical samples.
`zoom.prepare.process_SBP`(SBP, parcellation, ...)	Assign SBP image to parcellation image and perform spatial permutation test.
`zoom.prepare.fetch_medial_wall`(atlas, ...)	Fetch indices of medial wall vertices.

`zoom.pls_tool` - Imaging Transcriptomics

Functionality for performing cross-validation PLS-R and traditional imaging-transcriptomics paradigm.

`zoom.pls_tool.optimal_component_eval`(...)	Evaluate optimal component for PLS-R through cross-validation strategy.
`zoom.pls_tool.run_component_eval`(expression, ...)	Evaluate optimal component for PLS-R through cross-validation strategy.
`zoom.pls_tool.model_eval`(expression, SBP, ...)	Evaluate the final model performance for the PLS-R model.
`zoom.pls_tool.pls_perm`(expression, SBP, ...)	Perform spatial permutation test for PLS-R.
`zoom.pls_tool.vip_perm`(expression, SBP, ...)	Compute gene-level statistics and corresponding permutation p-values.
`zoom.pls_tool.boot_pls1`(expression, SBP, ...)	Estimate Z-scored PLS1 gene weights with bootstrap strategy.
`zoom.pls_tool.pls1_perm`(expression, SBP, ...)	Compute gene-level statistics and corresponding permutation p-values.

`zoom.sc_tool` - Single Cell Scoring

Functionality for preprocessing scRNA-seq data.

`zoom.sc_tool.preprocess`(adata, QC, ...)	Calculates the gene expression rank for each cell.
`zoom.sc_tool.rank_expression`(adata)	Calculates the gene expression rank for each cell.
`zoom.sc_tool.compute_gss`(adata, n_jobs)	Calculates the gene expression rank for each cell.
`zoom.sc_tool.select_ctrl`(weight_perm, ...)	Calculates the gene expression rank for each cell.
`zoom.sc_tool.score_cell_zoom`(adata, ...)	Calculates single-cell SBP-relevant enrichment scores.
`zoom.sc_tool.group_bh`(adata, df_res, pval, ...)	Perform group Benjamini–Hochberg FDR correction.
`zoom.sc_tool.downstream_DEG`(adata, df_res, ...)	Calculates differentially expressed genes (DEG) for cell groups containing cells significantly relevant to SBP.
`zoom.sc_tool.downstream_region_enrich`(adata, ...)	Computes region enrichment for cell groups containing significant cells based on predefined statistical results.
`zoom.sc_tool.gsea_perm`(gene_rep, weight_key, ...)	Permform GSEA based on spatial permutation test.