Overview
HeartMAP provides command-line tools for running single-cell RNA-seq analysis pipelines. The main CLI command allows you to analyze data directly from the terminal.
heartmap
The main command-line interface for running HeartMAP analysis pipelines.
Usage
heartmap <data_path> [OPTIONS]
Arguments
Path to the input data file (typically .h5ad format for AnnData objects).This is a positional argument and must be provided.
Examples
Basic Analysis
Run a basic analysis on your data:
heartmap data/heart_samples.h5ad --analysis-type basic
Starting basic analysis...
Loading data from data/heart_samples.h5ad...
Preprocessing: QC filtering...
Normalizing data...
Identifying highly variable genes...
Clustering cells...
Annotating cell types...
Analysis completed! Results saved to: results
Comprehensive Analysis
Run a comprehensive analysis with all pipeline components:
heartmap data/heart_samples.h5ad --analysis-type comprehensive --output-dir output/comprehensive
Starting comprehensive analysis...
Loading data from data/heart_samples.h5ad...
Running basic pipeline...
Analyzing cell-cell communication...
Performing multi-chamber analysis...
Generating visualizations...
Analysis completed! Results saved to: output/comprehensive
Multi-Chamber Analysis
Analyze chamber-specific patterns:
heartmap data/heart_chambers.h5ad --analysis-type multi_chamber --output-dir chambers_results
Starting multi_chamber analysis...
Loading data from data/heart_chambers.h5ad...
Identifying chamber-specific markers...
Analyzing chamber composition...
Detecting chamber-specific cell types...
Analysis completed! Results saved to: chambers_results
Custom Configuration
Use a custom configuration file:
heartmap data/heart_samples.h5ad --config config/custom_config.yaml --output-dir custom_results
Starting comprehensive analysis...
Loading configuration from config/custom_config.yaml...
Loading data from data/heart_samples.h5ad...
Applying custom parameters...
Analysis completed! Results saved to: custom_results
Output Structure
The CLI creates an output directory with the following structure:
results/
├── processed_data.h5ad # Processed AnnData object
├── annotation/ # Cell type annotation results
│ ├── cell_types.csv
│ └── markers.csv
├── communication/ # Cell-cell communication (if applicable)
│ ├── interactions.csv
│ └── networks/
├── multi_chamber/ # Multi-chamber analysis (if applicable)
│ ├── chamber_markers.csv
│ └── composition.csv
├── plots/ # Visualization outputs
│ ├── umap.png
│ ├── cell_types.png
│ └── ...
└── logs/ # Analysis logs
└── analysis.log
Exit Codes
0: Successful completion1: General error (invalid arguments, file not found, etc.)2: Configuration error (invalid config file)
See Also