snipit-mc 0.0.2

Enhanced snipit with artistic color palettes and improved SNP visualization

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

Gallery

Color Palette Comparison

Example Outputs

Nature Style - High-saturation colors for publications

Morandi Style - Muted, sophisticated tones

Van Gogh Style - Vibrant, expressive colors

GenBank Gene Annotations

SARS-CoV-2 Genome with Multi-color Gene Tracks

Nature Palette - High-saturation scientific colors

Morandi Palette - Muted, sophisticated tones

Monet Palette - Soft impressionist pastels

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

pip install snipit-mc

Or install directly from this repository:

git clone https://github.com/hyzhou1990/snipit-multicolor.git
cd snipit-multicolor
pip install -e .

Quick Start

Basic Usage

# 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

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

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

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

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

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

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

# 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

# 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

# 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:

# 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

snipit alignment.fasta --format pdf --output-file figure

Examples

Example 1: Publication-Ready Figure

snipit test.fasta \
  --colour-palette nature \
  --width 12 \
  --format pdf \
  --solid-background \
  --output-file publication_figure

Example 2: Amino Acid Alignment

snipit aa_alignment.fasta \
  --sequence-type aa \
  --colour-palette monet_aa \
  --sort-by-id \
  --output-file protein_analysis

Example 3: Custom Analysis

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

# 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.