API Reference

This section provides detailed API documentation for all gedi2py modules and functions.

• Core
  • GEDIModel
  • Settings
• Tools (gd.tl)
  • Model Training
  • Projections
  • Embeddings
  • Imputation
  • Differential Expression
  • Pathway Analysis
  • Dynamics / Trajectory
• Plotting (gd.pl)
  • Embedding Plots
  • Convergence Plots
  • Feature Plots
  • Common Parameters
• I/O (gd.io)
  • Reading Data
  • Writing Data
  • Model Persistence
  • Convenience Functions
  • File Formats
  • Workflow Example

Overview

gedi2py is organized into modules following the scanpy convention:

Module	Description
gedi2py	Top-level imports (GEDIModel, settings, I/O functions)
gedi2py.tl	Tools for model training, projections, embeddings, and analysis
gedi2py.pl	Plotting functions for visualization
gedi2py.io	Input/output for data and models

Import Convention

import gedi2py as gd

# Access modules
gd.tl.gedi(...)        # Tools
gd.pl.embedding(...)   # Plotting
gd.io.read_h5ad(...)   # I/O

# Or import directly
from gedi2py import GEDIModel
from gedi2py import settings

Quick Reference

Core

• GEDIModel - Main model class for GEDI analysis

Tools (gd.tl)

Model Training

• gedi() - Run GEDI batch correction

Projections

• get_projection() - Get computed projections

• compute_zdb() - Compute ZDB projection

• compute_db() - Compute DB projection

• compute_adb() - Compute ADB projection (pathway activity)

Embeddings

• svd() - Compute SVD on GEDI embedding

• pca() - Compute PCA on GEDI embedding

• umap() - Compute UMAP on GEDI embedding

Imputation

• impute() - Impute denoised expression

• variance() - Compute variance

• dispersion() - Compute dispersion

Differential Expression

• differential() - Differential expression analysis

• diff_q() - Sample-specific differential effects

• diff_o() - Offset differential effects

Pathway Analysis

• pathway_associations() - Compute pathway associations

• pathway_scores() - Compute pathway scores

• top_pathway_genes() - Get top genes per pathway

Dynamics

• vector_field() - Compute vector field

• gradient() - Compute gradient

• pseudotime() - Compute pseudotime

Plotting (gd.pl)

Embedding Plots

• embedding() - General embedding plot

• umap() - UMAP plot

• pca() - PCA plot

Convergence Plots

• convergence() - Plot convergence metrics

• loss() - Plot loss function

Feature Plots

• features() - Plot gene expression

• metagenes() - Plot metagene patterns

• dispersion() - Plot dispersion

• variance_explained() - Plot variance explained

I/O (gd.io)

Reading

• read_h5ad() - Read H5AD file

• read_10x_h5() - Read 10X H5 file

• read_10x_mtx() - Read 10X MTX directory

Writing

• write_h5ad() - Write H5AD file

Model Persistence

• save_model() - Save GEDI model

• load_model() - Load GEDI model