ManhattanPlot

A Manhattan plot displays GWAS p-values across the genome. Each point represents a SNP; the x-axis spans chromosomes and the y-axis shows −log₁₀(p-value). Dashed threshold lines are drawn automatically at genome-wide and suggestive significance levels. Chromosomes are colored with an alternating two-color scheme (or a full Palette).

Constructor

new

Create a Manhattan plot with default settings.

use kuva::plot::ManhattanPlot;

let mp = ManhattanPlot::new();

Returns: ManhattanPlot Defaults:

Genome-wide threshold: 7.301 (p = 5×10⁻⁸)
Suggestive threshold: 5.0 (p = 1×10⁻⁵)
Color A: "steelblue"
Color B: "#5aadcb"
Point size: 2.5
No labels, no legend

Data Input Methods

Three methods load data, each mapping (chrom, …, pvalue) onto the cumulative x-axis:

with_data

Input mode 1 — sequential integer x-coordinates.

pub fn with_data<I, S, G>(self, iter: I) -> Self
where
    I: IntoIterator<Item = (S, G)>,
    S: Into<String>,
    G: Into<f64>,

Accepts (chrom, pvalue) pairs. Chromosomes are sorted into standard genomic order (1–22, X, Y, MT); points within each chromosome receive consecutive integer x positions.

iter

impl IntoIterator<Item = (String, f64)>

Iterator of (chromosome_name, p_value) pairs

Use when: Base-pair positions are unavailable or unimportant. Example:

let data = vec![
    ("1".into(), 0.42), ("1".into(), 3e-8),
    ("2".into(), 0.17), ("2".into(), 5e-6),
];
let mp = ManhattanPlot::new().with_data(data);

with_data_bp

Input mode 2 — base-pair x-coordinates resolved from a reference genome build.

pub fn with_data_bp<I, S, F, G>(self, iter: I, build: GenomeBuild) -> Self
where
    I: IntoIterator<Item = (S, F, G)>,
    S: Into<String>,
    F: Into<f64>,
    G: Into<f64>,

Accepts (chrom, bp_position, pvalue) triplets. Each SNP’s x coordinate is computed as the chromosome’s cumulative offset plus its base-pair position.

iter

impl IntoIterator<Item = (String, f64, f64)>

Iterator of (chromosome_name, base_pair_position, p_value) triplets

build

GenomeBuild

Reference genome build (Hg19, Hg38, T2T, or Custom)

Use when: Standard GWAS output with base-pair positions. Example:

use kuva::plot::{ManhattanPlot, GenomeBuild};

let data = vec![("1", 100_000_000_f64, 3e-10_f64), ("6", 50_000_000_f64, 8e-9)];
let mp = ManhattanPlot::new().with_data_bp(data, GenomeBuild::Hg38);

with_data_x

Input mode 3 — pre-computed cumulative x-coordinates.

pub fn with_data_x<I, S, F, G>(self, iter: I) -> Self
where
    I: IntoIterator<Item = (S, F, G)>,
    S: Into<String>,
    F: Into<f64>,
    G: Into<f64>,

Accepts (chrom, x, pvalue) triplets where x is already in the cumulative coordinate system you want.

iter

impl IntoIterator<Item = (String, f64, f64)>

Iterator of (chromosome_name, cumulative_x, p_value) triplets

Use when: Custom or non-human genomes, or when you want full control over x positioning. Example:

let data = vec![
    ("A",  10.0_f64, 0.42_f64), ("A", 20.0, 3e-8),
    ("B", 120.0,     0.17),     ("B", 130.0, 5e-6),
];
let mp = ManhattanPlot::new().with_data_x(data);

Threshold Configuration

with_genome_wide

Set the genome-wide significance threshold in −log₁₀ scale.

pub fn with_genome_wide(self, threshold: f64) -> Self

threshold

f64

Significance threshold in −log₁₀ scale (default: 7.301 for p = 5×10⁻⁸)

A dashed red line is drawn at this y position. Only points above this threshold are candidates for with_label_top labels.

with_suggestive

Set the suggestive significance threshold in −log₁₀ scale.

pub fn with_suggestive(self, threshold: f64) -> Self

threshold

f64

Suggestive threshold in −log₁₀ scale (default: 5.0 for p = 1×10⁻⁵)

A dashed gray line is drawn at this y position.

Color Configuration

with_color_a

Set the color for even-indexed chromosomes (0, 2, 4, …).

pub fn with_color_a<S: Into<String>>(self, color: S) -> Self

color

String

CSS color string (default: "steelblue")

Ignored when a full Palette is set via with_palette.

with_color_b

Set the color for odd-indexed chromosomes (1, 3, 5, …).

pub fn with_color_b<S: Into<String>>(self, color: S) -> Self

color

String

CSS color string (default: "#5aadcb")

Ignored when a full Palette is set via with_palette.

with_palette

Override the alternating two-color scheme with a full palette.

pub fn with_palette(self, palette: Palette) -> Self

palette

Palette

Color palette (colors cycle with modulo wrapping across chromosomes)

Example:

use kuva::Palette;

let mp = ManhattanPlot::new()
    .with_data_bp(data, GenomeBuild::Hg38)
    .with_palette(Palette::tol_bright());

Point Configuration

with_point_size

Set the radius of each data point in pixels.

pub fn with_point_size(self, size: f64) -> Self

size

f64

Point radius in pixels (default: 2.5)

with_pvalue_floor

Set an explicit p-value floor for the −log₁₀ transform.

pub fn with_pvalue_floor(self, floor: f64) -> Self

floor

f64

Minimum p-value before log transformation

Points with pvalue == 0.0 are clamped to this value. When not set, the floor is inferred as the minimum non-zero p-value in the data.

Label Configuration

with_label_top

Label the n most significant points above the genome-wide threshold.

pub fn with_label_top(self, n: usize) -> Self

usize

Number of top points to label (default: 0)

Points are selected by lowest p-value among those exceeding genome_wide. Example:

let mp = ManhattanPlot::new()
    .with_data_bp(data, GenomeBuild::Hg38)
    .with_label_top(10);  // label the 10 most significant hits

with_label_style

Set the label placement style.

pub fn with_label_style(self, style: LabelStyle) -> Self

style

LabelStyle

Label placement style (default: LabelStyle::Nudge)

Options:

LabelStyle::Nudge — labels sorted by x and nudged vertically to reduce overlap (best default)
LabelStyle::Exact — labels at exact point position; may overlap
LabelStyle::Arrow { offset_x, offset_y } — labels offset by (offset_x, offset_y) px with a gray leader line

Example:

use kuva::plot::LabelStyle;

let mp = ManhattanPlot::new()
    .with_label_top(10)
    .with_label_style(LabelStyle::Arrow { offset_x: 10.0, offset_y: 14.0 });

with_point_labels

Attach gene or SNP labels to individual points by (chromosome, x, label).

pub fn with_point_labels<I, S, F, L>(self, iter: I) -> Self
where
    I: IntoIterator<Item = (S, F, L)>,
    S: Into<String>,
    F: Into<f64>,
    L: Into<String>,

iter

impl IntoIterator<Item = (String, f64, String)>

Iterator of (chromosome, x_position, label) triplets

The x value must match the coordinate assigned at data-load time. Matching uses a tolerance of ±0.5. Example:

let mp = ManhattanPlot::new()
    .with_data_x(data)
    .with_point_labels(vec![
        ("1",  40.0, "BRCA2"),
        ("2", 140.0, "TP53"),
    ]);

Legend

with_legend

Enable a legend showing genome-wide and suggestive threshold line entries.

pub fn with_legend<S: Into<String>>(self, label: S) -> Self

label

String

Legend label (must be set to enable the legend)

Example:

let mp = ManhattanPlot::new()
    .with_data_bp(data, GenomeBuild::Hg38)
    .with_legend("GWAS thresholds");

GenomeBuild Enum

Reference genome chromosome sizes used for cumulative x-coordinate layout.

Variants

GenomeBuild::Hg19 — GRCh37 / hg19 (24 chromosomes: 1–22, X, Y plus MT)
GenomeBuild::Hg38 — GRCh38 / hg38 (24 chromosomes: 1–22, X, Y plus MT)
GenomeBuild::T2T — T2T-CHM13 v2.0 / hs1 (complete telomere-to-telomere assembly)
GenomeBuild::Custom(Vec<(String, u64)>) — User-supplied (chrom_name, size_in_bp) list

Example:

use kuva::plot::GenomeBuild;

let build = GenomeBuild::Custom(vec![
    ("chr1".to_string(), 120_000_000),
    ("chr2".to_string(),  95_000_000),
    ("chrX".to_string(),  55_000_000),
]);

Full Example

use kuva::plot::{ManhattanPlot, GenomeBuild};
use kuva::backend::svg::SvgBackend;
use kuva::render::render::render_multiple;
use kuva::render::layout::Layout;
use kuva::render::plots::Plot;

// (chrom, bp_position, pvalue) triplets from PLINK/GCTA output
let data: Vec<(String, f64, f64)> = vec![];  // ...your data here

let mp = ManhattanPlot::new()
    .with_data_bp(data, GenomeBuild::Hg38)
    .with_label_top(10)
    .with_legend("GWAS thresholds");

let plots = vec![Plot::Manhattan(mp)];
let layout = Layout::auto_from_plots(&plots)
    .with_title("GWAS — Base-pair Coordinates (GRCh38)")
    .with_x_label("Chromosome")
    .with_y_label("−log₁₀(p-value)");

let svg = SvgBackend.render_scene(&render_multiple(plots, layout));
std::fs::write("manhattan.svg", svg).unwrap();

Core API

Plot APIs

Backends

Utilities

ManhattanPlot

Constructor

new

Data Input Methods

with_data

with_data_bp

with_data_x

Threshold Configuration

with_genome_wide

with_suggestive

Color Configuration

with_color_a

with_color_b

with_palette

Point Configuration

with_point_size

with_pvalue_floor

Label Configuration

with_label_top

with_label_style

with_point_labels

Legend

with_legend

GenomeBuild Enum

Variants

Full Example

Build docs developers (and LLMs) love

Core API

Plot APIs

Backends

Utilities

​Constructor

​new

​Data Input Methods

​with_data

​with_data_bp

​with_data_x

​Threshold Configuration

​with_genome_wide

​with_suggestive

​Color Configuration

​with_color_a

​with_color_b

​with_palette

​Point Configuration

​with_point_size

​with_pvalue_floor

​Label Configuration

​with_label_top

​with_label_style

​with_point_labels

​Legend

​with_legend

​GenomeBuild Enum

​Variants

​Full Example

Build docs developers (and LLMs) love

Constructor

new

Data Input Methods

with_data

with_data_bp

with_data_x

Threshold Configuration

with_genome_wide

with_suggestive

Color Configuration

with_color_a

with_color_b

with_palette

Point Configuration

with_point_size

with_pvalue_floor

Label Configuration

with_label_top

with_label_style

with_point_labels

Legend

with_legend

GenomeBuild Enum

Variants

Full Example