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CLI Reference

GGE provides a comprehensive command-line interface for running evaluations.

Basic Usage

gge --real <real_data.h5ad> --generated <generated_data.h5ad> --conditions <columns> --output <dir>

Arguments

Required Arguments

Argument Short Description
--real -r Path to real data file (h5ad format)
--generated -g Path to generated data file (h5ad format)
--conditions -c One or more condition columns for matching
--output -o Output directory for results

Optional Arguments

Argument Default Description
--split-column None Column name for train/test split
--splits all Which splits to evaluate (e.g., "test")
--metrics all Which metrics to compute
--n-genes all Number of genes to evaluate (random subset)
--seed 42 Random seed for reproducibility
--verbose False Print detailed progress
--version - Show version and exit

Examples

Basic Evaluation

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --output results/

Multiple Conditions

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation cell_type dose \
    --output results/

Test Set Only

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --split-column split \
    --splits test \
    --output results/

Specific Metrics

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --metrics pearson spearman wasserstein_1 \
    --output results/

Subset of Genes

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --n-genes 1000 \
    --seed 42 \
    --output results/

Verbose Output

gge --real real.h5ad --generated generated.h5ad \
    --conditions perturbation \
    --verbose \
    --output results/

Available Metrics

Use these names with --metrics:

  • pearson - Pearson correlation
  • spearman - Spearman correlation
  • wasserstein_1 - Wasserstein-1 distance
  • wasserstein_2 - Wasserstein-2 distance
  • mmd - Maximum Mean Discrepancy
  • energy - Energy distance

Exit Codes

Code Meaning
0 Success
1 Error (invalid arguments, file not found, etc.)

Environment Variables

Variable Description
GGE_SEED Default random seed
GGE_VERBOSE Default verbosity (0 or 1)