# snipit-multicolor
Enhanced version of snipit with artistic color palettes and improved visualization
Summarise SNPs relative to a reference sequence with beautiful, publication-ready visualizations
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/genome_graph.png" width="700">
## Gallery
### Color Palette Comparison
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/palette_comparison.png" width="800">
### Example Outputs
#### Nature Style - High-saturation colors for publications
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/nature_example.png" width="600">
#### Morandi Style - Muted, sophisticated tones
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/morandi_example.png" width="600">
#### Van Gogh Style - Vibrant, expressive colors
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/vangogh_example.png" width="600">
### GenBank Gene Annotations
#### SARS-CoV-2 Genome with Multi-color Gene Tracks
**Nature Palette** - High-saturation scientific colors
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_nature.png" width="700">
**Morandi Palette** - Muted, sophisticated tones
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_morandi.png" width="700">
**Monet Palette** - Soft impressionist pastels
<img src="https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_monet.png" width="700">
*Each gene (ORF1ab, S, ORF3a, E, M, N) receives its own unique color that harmonizes with the selected palette*
## What's New in snipit-multicolor
This enhanced version includes:
- **Artistic color palettes** inspired by famous painters (Morandi, Van Gogh, Monet, Matisse)
- **Enhanced visualization quality** with higher DPI, text shadows, and improved typography
- **Cleaner aesthetics** with removed outer borders and subtle label backgrounds
- **Better readability** with optimized font sizes and visual hierarchy
- **GenBank gene annotations** with multi-color gene tracks showing individual genes in harmonized colors
## Installation
### From PyPI (Recommended)
```bash
pip install snipit-mc
```
### From Source
```
git clone https://github.com/hyzhou1990/snipit-multicolor.git
cd snipit-multicolor
pip install -e .
```
## Quick Start
### Command Line Usage
```bash
# Basic nucleotide alignment visualization
snipit alignment.fasta --output-file output
# With artistic color palette
snipit alignment.fasta --colour-palette nature --output-file nature_plot
# For amino acid sequences
snipit protein.fasta --sequence-type aa --colour-palette nature_aa --output-file protein_plot
```
### Python API Usage
snipit-mc also provides a comprehensive Python API for programmatic use:
```python
from snipit import snipit_plot, SnipitConfig
# Basic usage
result = snipit_plot("alignment.fasta", colour_palette="nature")
# Advanced usage with configuration
config = SnipitConfig(
colour_palette="vangogh",
width=12,
height=8,
format="pdf",
genbank="reference.gb"
)
result = snipit_plot("alignment.fasta", config=config)
# Convenience functions
from snipit import quick_plot, publication_plot, protein_plot
# Quick plot
quick_plot("alignment.fasta", palette="nature")
# Publication-ready plot
publication_plot("alignment.fasta", palette="nature", genbank="ref.gb")
# Protein analysis
protein_plot("protein.fasta", palette="monet_aa")
```
📖 **[Complete Python API Documentation](docs/API_DOCUMENTATION.md)**
## Color Palettes
### Artistic Palettes
Each artistic palette is available in three versions:
- **Base version** for nucleotides (A, T, G, C)
- **Extended version** for ambiguous nucleotides
- **Amino acid version** for protein sequences
#### Nature Style
High-saturation colors suitable for Nature publications
```bash
snipit alignment.fasta --colour-palette nature # Nucleotides
snipit alignment.fasta --colour-palette nature_extended # With ambiguous bases
snipit protein.fasta --sequence-type aa --colour-palette nature_aa # Amino acids
```
#### Morandi Style
Muted, grey-toned colors inspired by Giorgio Morandi
```bash
snipit alignment.fasta --colour-palette morandi
snipit alignment.fasta --colour-palette morandi_extended
snipit protein.fasta --sequence-type aa --colour-palette morandi_aa
```
#### Van Gogh Style
Vibrant, expressive colors inspired by Vincent van Gogh
```bash
snipit alignment.fasta --colour-palette vangogh
snipit alignment.fasta --colour-palette vangogh_extended
snipit protein.fasta --sequence-type aa --colour-palette vangogh_aa
```
#### Monet Style
Soft impressionist pastels inspired by Claude Monet
```bash
snipit alignment.fasta --colour-palette monet
snipit alignment.fasta --colour-palette monet_extended
snipit protein.fasta --sequence-type aa --colour-palette monet_aa
```
#### Matisse Style
Bold, pure colors inspired by Henri Matisse
```bash
snipit alignment.fasta --colour-palette matisse
snipit alignment.fasta --colour-palette matisse_extended
snipit protein.fasta --sequence-type aa --colour-palette matisse_aa
```
### Classic Palettes
- `classic`: Traditional SNP visualization colors
- `classic_extended`: Classic with ambiguous base support
- `primary`: Primary colors
- `purine-pyrimidine`: Color by base type
- `greyscale`: Monochrome visualization
- `wes`: Wes Anderson inspired
- `verity`: Pink/purple theme
- `ugene`: UGENE software colors (for amino acids)
## Advanced Features
### Enhanced Visualization Options
```bash
# High-quality figure with custom size
snipit alignment.fasta \
--colour-palette nature \
--width 15 \
--height 10 \
--output-file high_quality
# Sort sequences by mutation count
snipit alignment.fasta \
--colour-palette vangogh \
--sort-by-mutation-number \
--output-file sorted_plot
```
### Working with Large Alignments
```bash
# Focus on specific regions
snipit large_alignment.fasta \
--colour-palette monet \
--include-positions 100-500 \
--exclude-positions 250-300 \
--output-file region_plot
# Include indels in visualization
snipit alignment.fasta \
--colour-palette matisse \
--show-indels \
--output-file indel_plot
```
### Recombination Analysis
```bash
# Visualize recombination patterns
snipit alignment.fasta \
--reference REF_SEQ \
--recombi-mode \
--recombi-references "PARENT1,PARENT2" \
--output-file recombination_plot
```
### Gene Annotations with GenBank
Display beautiful gene tracks with directional arrows using GenBank files:
```bash
# Add gene annotations from GenBank file
snipit alignment.fasta \
--genbank reference.gb \
--colour-palette nature \
--output-file annotated_plot
# Combine with other features
snipit alignment.fasta \
--genbank viral_genome.gb \
--colour-palette vangogh \
--sort-by-mutation-number \
--width 15 \
--output-file comprehensive_analysis
# Real example with SARS-CoV-2
snipit covid_sequences.fasta \
--genbank NC_045512.gb \
--colour-palette monet \
--output-file covid_with_genes
```
Each gene is automatically assigned a unique color that harmonizes with your chosen palette:
- **Nature palette**: High-saturation scientific colors
- **Morandi palette**: Muted, sophisticated tones
- **Van Gogh palette**: Vibrant, contrasting colors
- **Monet palette**: Soft impressionist pastels
- **Matisse palette**: Bold, pure colors
Arrows indicate gene direction (forward/reverse strand) and gene names are displayed when space permits.
## Output Formats
Supported output formats:
- `png` (default) - High-resolution raster image
- `pdf` - Vector format for publications
- `svg` - Editable vector format
- `jpg` - Compressed raster image
- `tiff` - High-quality raster for publications
```bash
snipit alignment.fasta --format pdf --output-file figure
```
## Examples
### Example 1: Publication-Ready Figure
```bash
snipit test.fasta \
--colour-palette nature \
--width 12 \
--format pdf \
--solid-background \
--output-file publication_figure
```
### Example 2: Amino Acid Alignment
```bash
snipit aa_alignment.fasta \
--sequence-type aa \
--colour-palette monet_aa \
--sort-by-id \
--output-file protein_analysis
```
### Example 3: Custom Analysis
```bash
snipit alignment.fasta \
--colour-palette vangogh_extended \
--reference "Reference_Seq" \
--labels sample_labels.csv \
--ambig-mode all \
--flip-vertical \
--output-file custom_analysis
```
### Example 4: SARS-CoV-2 with Gene Annotations
```bash
# Download SARS-CoV-2 reference GenBank file
curl -o NC_045512.gb "https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=NC_045512.2&db=nuccore&report=genbank&conwithfeat=on&hide-cdd=on&retmode=text"
# Create visualization with gene annotations
snipit covid_alignment.fasta \
--genbank NC_045512.gb \
--colour-palette nature \
--sort-by-mutation-number \
--width 14 \
--output-file covid_mutations_with_genes
```
## Full Usage
```
snipit <alignment> [options]
Input options:
alignment Input alignment fasta file
-t {nt,aa} Input sequence type: aa or nt (default: nt)
-r REFERENCE Reference sequence ID (default: first sequence)
-l LABELS CSV file with sequence labels
--l-header Column headers in label CSV (default: 'name,label')
-g, --genbank GenBank file for gene annotations
Output options:
-d OUTPUT_DIR Output directory (default: current directory)
-o OUTPUT_FILE Output file name stem (default: snp_plot)
-s, --write-snps Write SNPs to CSV file
-f FORMAT Output format: png, jpg, pdf, svg, tiff (default: png)
Figure options:
--height HEIGHT Figure height
--width WIDTH Figure width
--size-option Sizing options: expand, scale
--solid-background Solid background instead of transparent
-c, --colour-palette Color palette selection
--flip-vertical Flip plot orientation
--sort-by-mutation-number Sort by SNP count
--sort-by-id Sort alphabetically by ID
--sort-by-mutations Sort by bases at positions (e.g., '1,2,3')
SNP options:
--show-indels Include indels in plot
--include-positions Positions to include (e.g., '100-150')
--exclude-positions Positions to exclude (e.g., '223 224')
--ambig-mode Handle ambiguous bases: all, snps, exclude
```
## Citation
If you use snipit-multicolor in your work, please cite:
```
Original snipit:
Áine O'Toole, snipit (2024) GitHub repository, https://github.com/aineniamh/snipit
Enhanced multicolor version:
hyzhou1990, snipit-multicolor (2025) GitHub repository, https://github.com/hyzhou1990/snipit-multicolor
```
## Issues and Contributions
Please report issues or suggest features at: https://github.com/hyzhou1990/snipit-multicolor/issues
## License
This project maintains the same license as the original snipit tool.
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"description": "# snipit-multicolor\nEnhanced version of snipit with artistic color palettes and improved visualization\n\nSummarise SNPs relative to a reference sequence with beautiful, publication-ready visualizations\n\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/genome_graph.png\" width=\"700\">\n\n## Gallery\n\n### Color Palette Comparison\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/palette_comparison.png\" width=\"800\">\n\n### Example Outputs\n\n#### Nature Style - High-saturation colors for publications\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/nature_example.png\" width=\"600\">\n\n#### Morandi Style - Muted, sophisticated tones\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/morandi_example.png\" width=\"600\">\n\n#### Van Gogh Style - Vibrant, expressive colors\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/vangogh_example.png\" width=\"600\">\n\n### GenBank Gene Annotations\n\n#### SARS-CoV-2 Genome with Multi-color Gene Tracks\n\n**Nature Palette** - High-saturation scientific colors\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_nature.png\" width=\"700\">\n\n**Morandi Palette** - Muted, sophisticated tones\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_morandi.png\" width=\"700\">\n\n**Monet Palette** - Soft impressionist pastels\n<img src=\"https://raw.githubusercontent.com/hyzhou1990/snipit-multicolor/master/docs/examples/sars_cov2_monet.png\" width=\"700\">\n\n*Each gene (ORF1ab, S, ORF3a, E, M, N) receives its own unique color that harmonizes with the selected palette*\n\n## What's New in snipit-multicolor\n\nThis enhanced version includes:\n- **Artistic color palettes** inspired by famous painters (Morandi, Van Gogh, Monet, Matisse)\n- **Enhanced visualization quality** with higher DPI, text shadows, and improved typography\n- **Cleaner aesthetics** with removed outer borders and subtle label backgrounds\n- **Better readability** with optimized font sizes and visual hierarchy\n- **GenBank gene annotations** with multi-color gene tracks showing individual genes in harmonized colors\n\n## Installation\n\n### From PyPI (Recommended)\n```bash\npip install snipit-mc\n```\n\n### From Source\n```\ngit clone https://github.com/hyzhou1990/snipit-multicolor.git\ncd snipit-multicolor\npip install -e .\n```\n\n## Quick Start\n\n### Command Line Usage\n```bash\n# Basic nucleotide alignment visualization\nsnipit alignment.fasta --output-file output\n\n# With artistic color palette\nsnipit alignment.fasta --colour-palette nature --output-file nature_plot\n\n# For amino acid sequences\nsnipit protein.fasta --sequence-type aa --colour-palette nature_aa --output-file protein_plot\n```\n\n### Python API Usage\n\nsnipit-mc also provides a comprehensive Python API for programmatic use:\n\n```python\nfrom snipit import snipit_plot, SnipitConfig\n\n# Basic usage\nresult = snipit_plot(\"alignment.fasta\", colour_palette=\"nature\")\n\n# Advanced usage with configuration\nconfig = SnipitConfig(\n colour_palette=\"vangogh\",\n width=12,\n height=8,\n format=\"pdf\",\n genbank=\"reference.gb\"\n)\nresult = snipit_plot(\"alignment.fasta\", config=config)\n\n# Convenience functions\nfrom snipit import quick_plot, publication_plot, protein_plot\n\n# Quick plot\nquick_plot(\"alignment.fasta\", palette=\"nature\")\n\n# Publication-ready plot\npublication_plot(\"alignment.fasta\", palette=\"nature\", genbank=\"ref.gb\")\n\n# Protein analysis\nprotein_plot(\"protein.fasta\", palette=\"monet_aa\")\n```\n\n\ud83d\udcd6 **[Complete Python API Documentation](docs/API_DOCUMENTATION.md)**\n\n## Color Palettes\n\n### Artistic Palettes\nEach artistic palette is available in three versions:\n- **Base version** for nucleotides (A, T, G, C)\n- **Extended version** for ambiguous nucleotides\n- **Amino acid version** for protein sequences\n\n#### Nature Style\nHigh-saturation colors suitable for Nature publications\n```bash\nsnipit alignment.fasta --colour-palette nature # Nucleotides\nsnipit alignment.fasta --colour-palette nature_extended # With ambiguous bases\nsnipit protein.fasta --sequence-type aa --colour-palette nature_aa # Amino acids\n```\n\n#### Morandi Style\nMuted, grey-toned colors inspired by Giorgio Morandi\n```bash\nsnipit alignment.fasta --colour-palette morandi\nsnipit alignment.fasta --colour-palette morandi_extended\nsnipit protein.fasta --sequence-type aa --colour-palette morandi_aa\n```\n\n#### Van Gogh Style\nVibrant, expressive colors inspired by Vincent van Gogh\n```bash\nsnipit alignment.fasta --colour-palette vangogh\nsnipit alignment.fasta --colour-palette vangogh_extended\nsnipit protein.fasta --sequence-type aa --colour-palette vangogh_aa\n```\n\n#### Monet Style\nSoft impressionist pastels inspired by Claude Monet\n```bash\nsnipit alignment.fasta --colour-palette monet\nsnipit alignment.fasta --colour-palette monet_extended\nsnipit protein.fasta --sequence-type aa --colour-palette monet_aa\n```\n\n#### Matisse Style\nBold, pure colors inspired by Henri Matisse\n```bash\nsnipit alignment.fasta --colour-palette matisse\nsnipit alignment.fasta --colour-palette matisse_extended\nsnipit protein.fasta --sequence-type aa --colour-palette matisse_aa\n```\n\n### Classic Palettes\n- `classic`: Traditional SNP visualization colors\n- `classic_extended`: Classic with ambiguous base support\n- `primary`: Primary colors\n- `purine-pyrimidine`: Color by base type\n- `greyscale`: Monochrome visualization\n- `wes`: Wes Anderson inspired\n- `verity`: Pink/purple theme\n- `ugene`: UGENE software colors (for amino acids)\n\n## Advanced Features\n\n### Enhanced Visualization Options\n\n```bash\n# High-quality figure with custom size\nsnipit alignment.fasta \\\n --colour-palette nature \\\n --width 15 \\\n --height 10 \\\n --output-file high_quality\n\n# Sort sequences by mutation count\nsnipit alignment.fasta \\\n --colour-palette vangogh \\\n --sort-by-mutation-number \\\n --output-file sorted_plot\n```\n\n### Working with Large Alignments\n\n```bash\n# Focus on specific regions\nsnipit large_alignment.fasta \\\n --colour-palette monet \\\n --include-positions 100-500 \\\n --exclude-positions 250-300 \\\n --output-file region_plot\n\n# Include indels in visualization\nsnipit alignment.fasta \\\n --colour-palette matisse \\\n --show-indels \\\n --output-file indel_plot\n```\n\n### Recombination Analysis\n\n```bash\n# Visualize recombination patterns\nsnipit alignment.fasta \\\n --reference REF_SEQ \\\n --recombi-mode \\\n --recombi-references \"PARENT1,PARENT2\" \\\n --output-file recombination_plot\n```\n\n### Gene Annotations with GenBank\n\nDisplay beautiful gene tracks with directional arrows using GenBank files:\n\n```bash\n# Add gene annotations from GenBank file\nsnipit alignment.fasta \\\n --genbank reference.gb \\\n --colour-palette nature \\\n --output-file annotated_plot\n\n# Combine with other features\nsnipit alignment.fasta \\\n --genbank viral_genome.gb \\\n --colour-palette vangogh \\\n --sort-by-mutation-number \\\n --width 15 \\\n --output-file comprehensive_analysis\n\n# Real example with SARS-CoV-2\nsnipit covid_sequences.fasta \\\n --genbank NC_045512.gb \\\n --colour-palette monet \\\n --output-file covid_with_genes\n```\n\nEach gene is automatically assigned a unique color that harmonizes with your chosen palette:\n- **Nature palette**: High-saturation scientific colors\n- **Morandi palette**: Muted, sophisticated tones \n- **Van Gogh palette**: Vibrant, contrasting colors\n- **Monet palette**: Soft impressionist pastels\n- **Matisse palette**: Bold, pure colors\n\nArrows indicate gene direction (forward/reverse strand) and gene names are displayed when space permits.\n\n## Output Formats\n\nSupported output formats:\n- `png` (default) - High-resolution raster image\n- `pdf` - Vector format for publications\n- `svg` - Editable vector format\n- `jpg` - Compressed raster image\n- `tiff` - High-quality raster for publications\n\n```bash\nsnipit alignment.fasta --format pdf --output-file figure\n```\n\n## Examples\n\n### Example 1: Publication-Ready Figure\n```bash\nsnipit test.fasta \\\n --colour-palette nature \\\n --width 12 \\\n --format pdf \\\n --solid-background \\\n --output-file publication_figure\n```\n\n### Example 2: Amino Acid Alignment\n```bash\nsnipit aa_alignment.fasta \\\n --sequence-type aa \\\n --colour-palette monet_aa \\\n --sort-by-id \\\n --output-file protein_analysis\n```\n\n### Example 3: Custom Analysis\n```bash\nsnipit alignment.fasta \\\n --colour-palette vangogh_extended \\\n --reference \"Reference_Seq\" \\\n --labels sample_labels.csv \\\n --ambig-mode all \\\n --flip-vertical \\\n --output-file custom_analysis\n```\n\n### Example 4: SARS-CoV-2 with Gene Annotations\n```bash\n# Download SARS-CoV-2 reference GenBank file\ncurl -o NC_045512.gb \"https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=NC_045512.2&db=nuccore&report=genbank&conwithfeat=on&hide-cdd=on&retmode=text\"\n\n# Create visualization with gene annotations\nsnipit covid_alignment.fasta \\\n --genbank NC_045512.gb \\\n --colour-palette nature \\\n --sort-by-mutation-number \\\n --width 14 \\\n --output-file covid_mutations_with_genes\n```\n\n## Full Usage\n\n```\nsnipit <alignment> [options]\n\nInput options:\n alignment Input alignment fasta file\n -t {nt,aa} Input sequence type: aa or nt (default: nt)\n -r REFERENCE Reference sequence ID (default: first sequence)\n -l LABELS CSV file with sequence labels\n --l-header Column headers in label CSV (default: 'name,label')\n -g, --genbank GenBank file for gene annotations\n\nOutput options:\n -d OUTPUT_DIR Output directory (default: current directory)\n -o OUTPUT_FILE Output file name stem (default: snp_plot)\n -s, --write-snps Write SNPs to CSV file\n -f FORMAT Output format: png, jpg, pdf, svg, tiff (default: png)\n\nFigure options:\n --height HEIGHT Figure height\n --width WIDTH Figure width\n --size-option Sizing options: expand, scale\n --solid-background Solid background instead of transparent\n -c, --colour-palette Color palette selection\n --flip-vertical Flip plot orientation\n --sort-by-mutation-number Sort by SNP count\n --sort-by-id Sort alphabetically by ID\n --sort-by-mutations Sort by bases at positions (e.g., '1,2,3')\n\nSNP options:\n --show-indels Include indels in plot\n --include-positions Positions to include (e.g., '100-150')\n --exclude-positions Positions to exclude (e.g., '223 224')\n --ambig-mode Handle ambiguous bases: all, snps, exclude\n```\n\n## Citation\n\nIf you use snipit-multicolor in your work, please cite:\n\n```\nOriginal snipit:\n\u00c1ine O'Toole, snipit (2024) GitHub repository, https://github.com/aineniamh/snipit\n\nEnhanced multicolor version:\nhyzhou1990, snipit-multicolor (2025) GitHub repository, https://github.com/hyzhou1990/snipit-multicolor\n```\n\n## Issues and Contributions\n\nPlease report issues or suggest features at: https://github.com/hyzhou1990/snipit-multicolor/issues\n\n## License\n\nThis project maintains the same license as the original snipit tool.\n",
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