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SyntenyPlot visualizes collinear blocks between genomic sequences as horizontal bars connected by ribbon polygons. Each sequence is represented as a labeled horizontal bar, with ribbons connecting homologous regions. Inverted blocks (structural inversions) are drawn as crossed ribbons.

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When to Use

Synteny plots are ideal for:
  • Comparative genomics — chromosome rearrangements, conservation between species
  • Structural variation — inversions, translocations, duplications
  • Genome assembly validation — alignment between assemblies or scaffolds
  • Evolutionary analysis — synteny conservation across lineages
  • Ortholog mapping — visualizing conserved gene order between genomes

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Basic Example

use kuva::plot::synteny::SyntenyPlot;
use kuva::backend::svg::SvgBackend;
use kuva::render::render::render_multiple;
use kuva::render::layout::Layout;
use kuva::render::plots::Plot;

let plot = SyntenyPlot::new()
    .with_sequences([
        ("Human chr1", 248_956_422.0),
        ("Mouse chr1", 195_471_971.0),
    ])
    .with_block(0,  0.0,       50_000_000.0,  1,  0.0,       45_000_000.0)
    .with_block(0,  60_000_000.0, 120_000_000.0, 1, 55_000_000.0, 100_000_000.0)
    .with_block(0, 130_000_000.0, 200_000_000.0, 1, 110_000_000.0, 170_000_000.0);

let plots = vec![Plot::Synteny(plot)];
let layout = Layout::auto_from_plots(&plots)
    .with_title("Human chr1 vs Mouse chr1");

let svg = SvgBackend.render_scene(&render_multiple(plots, layout));
std::fs::write("synteny.svg", svg).unwrap();
By default, each sequence bar fills the full width (per-sequence scale). Use .with_shared_scale() for a shared coordinate ruler.

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Forward and Inverted Blocks

Inverted blocks (structural inversions) are drawn as crossed (bowtie) ribbons: 
let plot = SyntenyPlot::new()
    .with_sequences([("Seq A", 1_000_000.0), ("Seq B", 1_000_000.0)])
    .with_block(    0,       0.0, 200_000.0, 1,       0.0, 200_000.0)  // Forward
    .with_inv_block(0, 250_000.0, 500_000.0, 1, 250_000.0, 500_000.0)  // Inverted (crossed)
    .with_block(    0, 600_000.0, 900_000.0, 1, 600_000.0, 900_000.0); // Forward
  • Forward blocks (.with_block()): Ribbons connect directly (parallel)
  • Inverted blocks (.with_inv_block()): Ribbons cross (bowtie shape)

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Three-Way Synteny

Visualize synteny across multiple sequences: 
let plot = SyntenyPlot::new()
    .with_sequences([
        ("Genome A", 500_000.0),
        ("Genome B", 480_000.0),
        ("Genome C", 450_000.0),
    ])
    // Blocks between Genome A (seq 0) and Genome B (seq 1)
    .with_block(    0,       0.0, 100_000.0, 1,       0.0,  95_000.0)
    .with_block(    0, 150_000.0, 300_000.0, 1, 140_000.0, 280_000.0)
    // Blocks between Genome B (seq 1) and Genome C (seq 2)
    .with_block(    1,       0.0, 100_000.0, 2,   5_000.0, 105_000.0)
    .with_inv_block(1, 200_000.0, 350_000.0, 2, 190_000.0, 340_000.0);

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Custom Colors

Set sequence bar colors and per-block colors: 
let plot = SyntenyPlot::new()
    .with_sequences([("Seq 1", 500_000.0), ("Seq 2", 500_000.0)])
    .with_sequence_colors(["#4393c3", "#d6604d"])  // Bar colors
    .with_colored_block(    0,       0.0, 150_000.0, 1,       0.0, 150_000.0, "#2ca02c")  // Green block
    .with_colored_block(    0, 200_000.0, 350_000.0, 1, 200_000.0, 340_000.0, "#9467bd")  // Purple block
    .with_colored_inv_block(0, 380_000.0, 480_000.0, 1, 370_000.0, 470_000.0, "#ff7f0e")  // Orange inverted
    .with_legend("Blocks");

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Shared Scale

By default, each sequence bar fills the full width (per-sequence scale). Enable shared scale for a common coordinate ruler: 
let plot = SyntenyPlot::new()
    .with_sequences([
        ("Chr 1", 100_000_000.0),
        ("Chr 2",  80_000_000.0),  // Shorter — will draw narrower bar
    ])
    .with_shared_scale();  // All sequences use the same coordinate scale
With shared scale, shorter sequences draw narrower bars, making length differences visible.

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Key Methods

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SyntenyPlot::new()

Create a synteny plot with default settings:
  • Bar height: 18.0 pixels
  • Block opacity: 0.65
  • Shared scale: false (per-sequence scale)

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.with_sequences<S, L>(seqs: impl IntoIterator<Item = (S, L)>)

Add sequences from (label, length) pairs. Sequences are indexed in the order added (0-indexed). 
let plot = SyntenyPlot::new()
    .with_sequences([
        ("Human chr1", 248_956_422.0),  // Sequence 0
        ("Mouse chr1", 195_471_971.0),  // Sequence 1
    ]);

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.with_sequence_colors<C: Into<String>>(colors: impl IntoIterator<Item = C>)

Override sequence bar colors. Provide one color per sequence in the same order. 
let plot = SyntenyPlot::new()
    .with_sequences(seqs)
    .with_sequence_colors(["#e41a1c", "#377eb8", "#4daf4a"]);

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.with_block(seq1: usize, start1: f64, end1: f64, seq2: usize, start2: f64, end2: f64)

Add a forward (parallel) collinear block between two sequences.
  • seq1, seq2: Sequence indices (0-indexed)
  • start1, end1: Coordinates on sequence 1
  • start2, end2: Coordinates on sequence 2
let plot = SyntenyPlot::new()
    .with_sequences(seqs)
    .with_block(0, 1000.0, 5000.0, 1, 2000.0, 6000.0);  // Forward block

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.with_inv_block(seq1: usize, start1: f64, end1: f64, seq2: usize, start2: f64, end2: f64)

Add an inverted (crossed) block, indicating a structural inversion. 
let plot = SyntenyPlot::new()
    .with_sequences(seqs)
    .with_inv_block(0, 10000.0, 20000.0, 1, 15000.0, 25000.0);  // Inversion

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.with_colored_block(seq1, start1, end1, seq2, start2, end2, color)

Add a forward block with an explicit color. 
let plot = SyntenyPlot::new()
    .with_sequences(seqs)
    .with_colored_block(0, 0.0, 1000.0, 1, 0.0, 1000.0, "#ff5733");

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.with_colored_inv_block(seq1, start1, end1, seq2, start2, end2, color)

Add an inverted block with an explicit color.

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.with_blocks(blocks: impl IntoIterator<Item = SyntenyBlock>)

Batch-add pre-built SyntenyBlock structures: 
let blocks = vec![
    SyntenyBlock {
        seq1: 0, start1: 0.0, end1: 1000.0,
        seq2: 1, start2: 0.0, end2: 1000.0,
        strand: Strand::Forward,
        color: None,
    },
];
let plot = SyntenyPlot::new()
    .with_sequences(seqs)
    .with_blocks(blocks);

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.with_bar_height(h: f64)

Set sequence bar height in pixels (default 18.0).

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.with_opacity(opacity: f64)

Set ribbon fill opacity (default 0.65). Range: 0.0 (transparent) to 1.0 (opaque).

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.with_shared_scale()

Enable shared coordinate ruler. By default, each sequence bar fills the full width (per-sequence scale). With shared scale, shorter sequences draw narrower bars.

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.with_legend<S: Into<String>>(label: S)

Add a legend (useful when using colored blocks or sequence colors).

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Data Structures

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SyntenyPlot

pub struct SyntenyPlot {
    pub sequences: Vec<SyntenySequence>,
    pub blocks: Vec<SyntenyBlock>,
    pub bar_height: f64,        // Pixel height of each sequence bar
    pub block_opacity: f64,     // Ribbon fill-opacity
    pub shared_scale: bool,     // false = per-sequence scale; true = shared ruler
    pub legend_label: Option<String>,
}

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SyntenySequence

pub struct SyntenySequence {
    pub label: String,
    pub length: f64,           // Sequence length in base pairs
    pub color: Option<String>, // Bar fill color
}

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SyntenyBlock

pub struct SyntenyBlock {
    pub seq1: usize,           // Sequence index (0-indexed)
    pub start1: f64,
    pub end1: f64,
    pub seq2: usize,
    pub start2: f64,
    pub end2: f64,
    pub strand: Strand,        // Forward or Reverse
    pub color: Option<String>, // Ribbon fill color
}

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Strand

pub enum Strand {
    Forward,  // Parallel ribbon
    Reverse,  // Crossed (bowtie) ribbon
}

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Tips

  • Block direction: Use inverted blocks (.with_inv_block()) to highlight structural inversions
  • Coordinate system: Start and end coordinates are in base pairs; use actual genomic coordinates
  • Scale mode: Use per-sequence scale (default) when comparing sequences of similar length; use shared scale when length differences are important
  • Color strategy: Use per-block colors to highlight functional regions (genes, repeats, conservation levels)
  • Opacity: Reduce opacity if blocks overlap heavily
  • Multiple sequences: Connect adjacent pairs (seq 0-1, 1-2, 2-3) for multi-way comparisons
  • Gaps: Absence of ribbons indicates non-syntenic regions or assembly gaps
  • Resolution: For whole-genome comparisons, use blocks > 10kb to avoid visual clutter

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Parsing Synteny Data

Common formats for synteny data:

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MCScanX format

## Alignment 1
0 - 0   seq1:gene1   seq2:gene1   0.95
0 - 1   seq1:gene2   seq2:gene2   0.88

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LASTZ/Chain format

Extract block coordinates from alignment chains.

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MUMmer/nucmer

Parse .delta or .coords files to extract collinear blocks.

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