richAnn 1.0.0

Functional enrichment analysis and visualization for Python

richAnn

Rich Annotation: Functional Enrichment Analysis and Visualization for Python

Overview

richAnn is a comprehensive Python package for gene set enrichment analysis, providing powerful statistical methods and publication-quality visualizations. Inspired by the R package richR, richAnn brings advanced enrichment analysis capabilities to the Python ecosystem.

Key Features

• Multiple Enrichment Methods

  • Gene Ontology (GO) enrichment analysis
  • KEGG pathway analysis
  • Gene Set Enrichment Analysis (GSEA) with permutation testing

• Advanced Analysis

  • Kappa-based term clustering to group similar results
  • Cross-sample comparison for differential enrichment
  • Multiple testing correction (Benjamini-Hochberg, Bonferroni, etc.)

• Publication-Quality Visualizations

  • Bar plots and dot plots for enrichment results
  • Network graphs (term-gene, term-term, multi-database networks)
  • Heatmaps for cross-sample comparison
  • GSEA enrichment score plots

• Flexible Data Loading

  • GMT file support for custom gene sets
  • GAF file parser for GO annotations
  • KEGG mapping file support
  • Custom annotation builder

Installation

From Source

git clone https://github.com/guokai8/richAnn.git
cd richAnn
pip install -e .

Development Installation

To install with development dependencies (pytest, black, flake8):

pip install -e ".[dev]"

Dependencies

• Python ≥ 3.8
• numpy ≥ 1.21.0
• pandas ≥ 1.3.0
• scipy ≥ 1.7.0
• matplotlib ≥ 3.4.0
• seaborn ≥ 0.11.0
• networkx ≥ 2.6.0
• statsmodels ≥ 0.13.0

Quick Start

Basic GO Enrichment Analysis

import richAnn as ra
import pandas as pd

# Your gene list of interest
genes = ["BRCA1", "BRCA2", "TP53", "ATM", "CHEK2", "RAD51", "PALB2"]

# Load GO annotation (or prepare your own DataFrame)
go_data = pd.DataFrame({
    'GeneID': ['BRCA1', 'BRCA2', 'TP53', 'ATM', ...],
    'GOterm': ['GO:0006281', 'GO:0006281', ...],
    'GOname': ['DNA repair', 'DNA repair', ...],
    'Ontology': ['BP', 'BP', ...]
})

# Perform GO enrichment
result = ra.richGO(
    genes=genes,
    godata=go_data,
    ontology="BP",  # Biological Process
    pvalue=0.05,
    padj=0.05,
    minSize=5,
    maxSize=500
)

# View results
print(result)
result.summary()

# Export results
result.to_csv("go_enrichment_results.csv")

Visualize Results

# Bar plot
fig = ra.ggbar(result, top=10, filename="barplot.png")

# Dot plot
fig = ra.ggdot(result, top=10, filename="dotplot.png")

# Network visualization
fig = ra.ggnetwork(result, top=20, filename="network.png")

KEGG Pathway Enrichment

# Load KEGG annotation
kegg_data = pd.DataFrame({
    'GeneID': ['BRCA1', 'BRCA2', ...],
    'Pathway': ['hsa03440', 'hsa03440', ...],
    'PathwayName': ['Homologous recombination', ...]
})

# Perform KEGG enrichment
kegg_result = ra.richKEGG(
    genes=genes,
    kodata=kegg_data,
    pvalue=0.05,
    padj=0.05
)

Gene Set Enrichment Analysis (GSEA)

# Gene scores (e.g., from differential expression analysis)
gene_scores = {
    "BRCA1": 2.5,
    "BRCA2": 2.3,
    "TP53": 2.1,
    "CDK1": -1.8,
    "CDK2": -1.5,
    # ... more genes
}

# Load gene set database
geneset_db = pd.DataFrame({
    'GeneSet': ['DNA_REPAIR', 'DNA_REPAIR', ...],
    'GeneSetName': ['DNA repair pathway', ...],
    'GeneID': ['BRCA1', 'BRCA2', ...]
})

# Perform GSEA
gsea_result = ra.richGSEA(
    gene_scores=gene_scores,
    geneset_db=geneset_db,
    nperm=1000,
    min_size=15,
    max_size=500
)

# Visualize specific pathway
fig = ra.ggGSEA(gsea_result, gene_scores, term_id="DNA_REPAIR")

Advanced Features

Term Clustering

Cluster similar enrichment terms based on gene overlap:

# Cluster enrichment results
clustered = ra.richCluster(
    result,
    cutoff=0.5,      # Kappa score threshold
    minSize=5,       # Minimum cluster size
    escore=3         # Enrichment score cutoff (-log10(padj))
)

# Visualize clustered network
fig = ra.ggnetwork(clustered, top=30)

Cross-Sample Comparison

Compare enrichment across multiple conditions:

# Perform enrichment for multiple samples
sample1_result = ra.richGO(sample1_genes, go_data, ontology="BP")
sample2_result = ra.richGO(sample2_genes, go_data, ontology="BP")
sample3_result = ra.richGO(sample3_genes, go_data, ontology="BP")

# Compare results
comparison = ra.compareResult({
    'Control': sample1_result,
    'Treatment1': sample2_result,
    'Treatment2': sample3_result
})

# Visualize comparison
fig = ra.ggheatmap(comparison, top=30)
fig = ra.comparedot(comparison, top=10)

Load Annotations from Standard Formats

# Load from GMT file (e.g., MSigDB)
geneset_db = ra.load_gmt("c2.cp.kegg.v7.4.symbols.gmt")

# Load GO annotations from GAF file
go_data = ra.load_go_gaf(
    "goa_human.gaf",
    ontology="BP",
    evidence_codes=["EXP", "IDA", "IPI", "IMP", "IGI", "IEP"]
)

# Load KEGG pathway mapping
kegg_data = ra.load_kegg_mapping("kegg_human.txt", organism="hsa")

# Create custom annotation
custom_sets = {
    "DNA_REPAIR": ["BRCA1", "BRCA2", "TP53", "ATM"],
    "CELL_CYCLE": ["CDK1", "CDK2", "CCNA1", "CCNB1"]
}
custom_annot = ra.create_custom_annotation(custom_sets)

Validate Annotation Quality

# Validate annotation format and get statistics
stats = ra.validate_annotation_format(
    go_data,
    required_cols=['GeneID', 'GOterm', 'GOname', 'Ontology']
)

print(f"Valid: {stats['valid']}")
print(f"Unique genes: {stats['n_genes']}")
print(f"Unique annotations: {stats['n_annotations']}")
print(f"Warnings: {stats['warnings']}")

Integration with pathwaydb

richAnn integrates seamlessly with pathwaydb, a lightweight Python library for downloading and querying biological pathway annotations. This is the recommended approach for production use.

Why Use pathwaydb?

• Easy setup: Download annotations with one command
• Offline access: Query locally without internet
• Always up-to-date: Fresh data from official sources (GO, KEGG)
• 12 model species: Human, mouse, rat, zebrafish, fly, worm, yeast, and more
• Fast queries: Millisecond lookups on SQLite databases

Installation

# Install pathwaydb
pip install pathwaydb

# Or install from source
git clone https://github.com/guokai8/pathwaydb.git
cd pathwaydb && pip install -e .

Quick Start with pathwaydb

GO Enrichment Analysis

import richAnn as ra
from pathwaydb import GO

# Step 1: Download GO annotations (only needed once)
go = GO(storage_path='go_human.db')
go.download_annotations(species='human')
# Output: Downloaded 500,000+ annotations with term names

# Step 2: Convert to richAnn format
go_data = ra.from_pathwaydb_go(go.storage, ontology="BP")
print(f"Loaded {go_data['GOterm'].nunique()} GO terms for {go_data['GeneID'].nunique()} genes")

# Step 3: Run enrichment analysis
genes = ["BRCA1", "BRCA2", "TP53", "ATM", "CHEK2", "RAD51", "PALB2", "NBN"]
result = ra.richGO(genes, go_data, ontology="BP", pvalue=0.05, padj=0.1)

# Step 4: View and visualize results
print(result)
result.summary()
fig = ra.ggdot(result, top=15)

KEGG Pathway Enrichment

import richAnn as ra
from pathwaydb import KEGG

# Step 1: Download KEGG annotations (includes pathway hierarchy!)
kegg = KEGG(species='hsa', storage_path='kegg_human.db')
kegg.download_annotations()  # Automatically downloads pathway hierarchy
kegg.convert_ids_to_symbols()  # Convert Entrez IDs to gene symbols

# Step 2: Convert to richAnn format
kegg_data = ra.from_pathwaydb_kegg(kegg.storage)
print(f"Loaded {kegg_data['Pathway'].nunique()} pathways")

# Step 3: Run enrichment analysis
result = ra.richKEGG(genes, kegg_data, pvalue=0.05)

# Step 4: Results now include pathway hierarchy!
print(result.result[['Annot', 'Term', 'Level1', 'Level2', 'Padj']].head())
#         Annot                    Term           Level1                  Level2      Padj
# 0   hsa03440  Homologous recombination  Genetic Info...  Replication and repair  0.0001
# 1   hsa04110              Cell cycle    Cellular Processes        Cell growth...  0.0005

# Step 5: Visualize
fig = ra.ggbar(result, top=10)
fig = ra.ggnetwork(result, top=20)

KEGG Pathway Hierarchy Levels:

• Level1: Top-level category (e.g., "Metabolism", "Human Diseases", "Cellular Processes")
• Level2: Sub-category (e.g., "Carbohydrate metabolism", "Cancer", "Cell growth and death")
• Level3: Pathway name (same as PathwayName)

Complete Workflow Example

import richAnn as ra
from pathwaydb import GO, KEGG

# =============================================================================
# Setup: Download annotations (run once, data is cached locally)
# =============================================================================

# GO annotations
go = GO(storage_path='go_human.db')
go.download_annotations(species='human')

# KEGG annotations
kegg = KEGG(species='hsa', storage_path='kegg_human.db')
kegg.download_annotations()
kegg.convert_ids_to_symbols()

# =============================================================================
# Analysis: Your gene list (e.g., from differential expression)
# =============================================================================

# Example: DNA damage response genes
my_genes = [
    "TP53", "BRCA1", "BRCA2", "ATM", "ATR", "CHEK1", "CHEK2",
    "RAD51", "PALB2", "NBN", "MRE11", "RAD50", "XRCC1", "PARP1"
]

# =============================================================================
# GO Enrichment (Biological Process)
# =============================================================================

go_data = ra.from_pathwaydb_go(go.storage, ontology="BP")
go_result = ra.richGO(
    genes=my_genes,
    godata=go_data,
    ontology="BP",
    pvalue=0.05,
    padj=0.1,
    minSize=5,
    maxSize=500
)

print("=== GO Enrichment Results ===")
go_result.summary()

# Top enriched terms
print("\nTop 10 GO Terms:")
for _, row in go_result.top(10).result.iterrows():
    print(f"  {row['Annot']}: {row['Term']} (Padj={row['Padj']:.2e})")

# =============================================================================
# KEGG Enrichment
# =============================================================================

kegg_data = ra.from_pathwaydb_kegg(kegg.storage)
kegg_result = ra.richKEGG(
    genes=my_genes,
    kodata=kegg_data,
    pvalue=0.05,
    padj=0.1
)

print("\n=== KEGG Enrichment Results ===")
kegg_result.summary()

# =============================================================================
# Visualizations
# =============================================================================

# GO dot plot
fig_go = ra.ggdot(go_result, top=15, usePadj=True)
fig_go.savefig("go_dotplot.png", dpi=300, bbox_inches='tight')

# KEGG bar plot
fig_kegg = ra.ggbar(kegg_result, top=10, colorBy='Padj')
fig_kegg.savefig("kegg_barplot.png", dpi=300, bbox_inches='tight')

# Combined network
fig_net = ra.ggnetmap(
    {'GO': go_result, 'KEGG': kegg_result},
    top=10
)
fig_net.savefig("combined_network.png", dpi=300, bbox_inches='tight')

# =============================================================================
# Export Results
# =============================================================================

go_result.to_csv("go_enrichment_results.csv")
kegg_result.to_csv("kegg_enrichment_results.csv")

Multi-Species Analysis

pathwaydb supports 12 model organisms. Use the same workflow for any species:

from pathwaydb import GO, get_supported_species

# List all supported species
print(get_supported_species())
# ['arabidopsis', 'chicken', 'cow', 'dog', 'fly', 'human', 'mouse', 'pig', 'rat', 'worm', 'yeast', 'zebrafish']

# Mouse analysis
go_mouse = GO(storage_path='go_mouse.db')
go_mouse.download_annotations(species='mouse')
go_data_mouse = ra.from_pathwaydb_go(go_mouse.storage, ontology="BP")

# Zebrafish analysis
go_zebrafish = GO(storage_path='go_zebrafish.db')
go_zebrafish.download_annotations(species='zebrafish')
go_data_zebrafish = ra.from_pathwaydb_go(go_zebrafish.storage, ontology="BP")

# Fly (Drosophila) analysis
go_fly = GO(storage_path='go_fly.db')
go_fly.download_annotations(species='fly')
go_data_fly = ra.from_pathwaydb_go(go_fly.storage, ontology="BP")

Using Cached Annotations

For repeated analyses, use pathwaydb's centralized cache:

from pathwaydb import GO

# Load from cache (auto-downloads if not cached)
go = GO.from_cache(species='human')

# Convert and analyze
go_data = ra.from_pathwaydb_go(go.storage, ontology="BP")
result = ra.richGO(genes, go_data, ontology="BP")

Filter GO by Evidence Codes

# Download with all evidence codes
go = GO(storage_path='go_human.db')
go.download_annotations(species='human')

# Filter for experimental evidence only during conversion
go_data = ra.from_pathwaydb_go(go.storage, ontology="BP")

# Or filter using pathwaydb before conversion
experimental = go.storage.filter(evidence_codes=['EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP'])
# Then manually build DataFrame if needed

pathwaydb Data Format Reference

GO columns from pathwaydb:

pathwaydb	richAnn	Description
GeneID	GeneID	Gene symbol
TERM	GOterm	GO term ID (GO:0006281)
Aspect	Ontology	P→BP, F→MF, C→CC
term_name	GOname	Term description

KEGG columns from pathwaydb:

pathwaydb	richAnn	Description
GeneID	GeneID	Gene symbol
PATH	Pathway	Pathway ID (hsa04110)
Annot	PathwayName	Pathway name
Level1	Level1	Top-level category (e.g., "Metabolism")
Level2	Level2	Sub-category (e.g., "Carbohydrate metabolism")
Level3	Level3	Pathway name (same as PathwayName)

Working with EnrichResult Objects

EnrichResult is the core data structure returned by all enrichment functions:

# Filter results
filtered = result.filter(
    pvalue=0.01,           # P-value cutoff
    padj=0.05,             # Adjusted p-value cutoff
    min_count=5,           # Minimum gene count
    min_richfactor=1.5     # Minimum enrichment factor
)

# Get top N results
top10 = result.top(n=10, orderby='Padj')

# Get gene-term details
detail_df = result.detail()  # Returns DataFrame with one row per gene-term pair

# Print summary statistics
result.summary()

# Export to various formats
result.to_csv("results.csv")
result.to_excel("results.xlsx", sheet_name="GO_BP")

# Access underlying DataFrame
df = result.result
print(df.columns)  # View available columns

Visualization Gallery

Bar Plot

ra.ggbar(result, top=15, colorBy='Padj', horiz=True, filename="barplot.pdf", dpi=300)

Dot Plot

ra.ggdot(result, top=15, usePadj=True, size_range=(50, 500), filename="dotplot.pdf")

Term-Gene Network

ra.ggnetplot(result, top=20, layout='spring', filename="term_gene_network.pdf")

Term-Term Similarity Network

ra.ggnetwork(result, top=30, weightcut=0.2, layout='spring', filename="term_network.pdf")

Multi-Database Network

ra.ggnetmap(
    {'GO': go_result, 'KEGG': kegg_result},
    top=15,
    filename="combined_network.pdf"
)

Comparison Heatmap

ra.ggheatmap(
    comparison_df,
    top=30,
    cluster_rows=True,
    cluster_cols=False,
    filename="heatmap.pdf"
)

Understanding the Results

Key Columns in Results

• Annot: Annotation ID (e.g., GO:0006281, hsa03440)
• Term: Human-readable term name
• Pvalue: Raw p-value from hypergeometric test
• Padj: Adjusted p-value (Benjamini-Hochberg FDR by default)
• Count: Number of query genes in this term
• GeneID: Semicolon-separated list of genes
• RichFactor: Enrichment ratio (observed/expected)
• GeneRatio: Query genes in term / total query genes (k/n)
• BgRatio: Background genes in term / total background (M/N)
• OddsRatio: Odds ratio from Fisher's exact test

Statistical Methods

Hypergeometric Test (richGO, richKEGG)

Tests for over-representation using the hypergeometric distribution:

• P(X ≥ k) where k = number of overlapping genes
• Accounts for gene set size and background universe

GSEA (richGSEA)

Ranks genes by score and calculates enrichment score:

• Weighted running sum based on gene ranks
• Permutation testing for significance
• Normalized enrichment score (NES) accounts for gene set size

Tips and Best Practices

1. Choose Appropriate Background

# Option 1: Use all genes in annotation (default)
result = ra.richGO(genes, go_data, ontology="BP")

# Option 2: Provide custom background (recommended for RNA-seq)
background = list(expressed_genes)  # All genes detected in experiment
result = ra.richGO(genes, go_data, ontology="BP", universe=background)

2. Handle Gene ID Formatting

# Case-insensitive matching (default)
result = ra.richGO(genes, go_data, case_sensitive=False)

# Case-sensitive matching
result = ra.richGO(genes, go_data, case_sensitive=True)

3. Adjust Gene Set Size Limits

# Exclude very small and very large gene sets
result = ra.richGO(
    genes, go_data,
    minSize=10,   # Exclude terms with < 10 genes
    maxSize=300   # Exclude terms with > 300 genes
)

4. Multiple Testing Correction

# Benjamini-Hochberg FDR (default)
result = ra.richGO(genes, go_data, padj_method="BH")

# Bonferroni correction (more conservative)
result = ra.richGO(genes, go_data, padj_method="bonferroni")

# No correction (use with caution)
result = ra.richGO(genes, go_data, padj_method="none")

Common Issues and Solutions

Issue: "No query genes found in background universe"

Solution: Check gene ID format matches annotation. Try case_sensitive=False.

Issue: "No enriched terms found"

Solutions:

• Relax p-value cutoff: pvalue=0.1
• Adjust gene set size limits: minSize=3, maxSize=1000
• Check that your gene list is biologically relevant
• Verify annotation database matches your organism

Issue: GSEA is slow

Solution: Reduce permutations (but keep ≥ 1000): nperm=1000

Issue: Visualizations have overlapping labels

Solutions:

• Reduce top parameter: top=10
• Increase figure size: figsize=(14, 10)
• Decrease font size: fontsize=8

Testing

Run the test suite:

# Run all tests
pytest

# Run with coverage
pytest --cov=richAnn

# Run specific test file
pytest tests/test_enrichment.py

# Run with verbose output
pytest -v

Development

Code Formatting

black richAnn/

Linting

flake8 richAnn/

Citation

If you use richAnn in your research, please cite:

[Citation information will be added upon publication]

Contributing

Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Acknowledgments

• Inspired by the R package richR
• Built on the excellent scientific Python ecosystem (NumPy, pandas, SciPy, matplotlib)

Contact

For questions and feedback:

• Open an issue on GitHub
• Email: [e-mail]

Changelog

Version 1.0.0 (Current)

New Features

• GO, KEGG, and GSEA enrichment analysis
• Kappa-based term clustering
• 8 visualization types
• GMT, GAF, and KEGG file loaders
• Custom annotation builder
• Cross-sample comparison tools
• Comprehensive test suite

Bug Fixes

• Fixed module import error
• Improved GSEA performance (28x faster)
• Added edge case handling for visualizations
• Enhanced error messages with actionable suggestions

Improvements

• Added input validation for all functions
• Comprehensive documentation with examples
• Test coverage for core functionality
• Better error handling throughout

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Happy Enriching! 🧬