Linkage disequilibrium plot

Generates a static LD heatmap from a pre-computed LDResults object using ggplot2 graphics.

Usage

plotLD(
  ldObj,
  plotVal = c("r2", "DPrime", "pDiseq"),
  colorScheme = c("viridis", "magma", "inferno", "plasma", "cividis", "rocket", "mako",
    "turbo", "haploview"),
  ldBlocks = NULL,
  genomicTrack = FALSE,
  showIndex = TRUE,
  verbose = TRUE
)

Arguments

ldObj

An object of class LDResults as returned by linkageDiseq.

plotVal

What LD value do you want to plot? Options are:

• r2: \(r^{2}\) (Default parameter)

• DPrime: \(D'\)

• pDiseq: p-value

colorScheme

Color palette for the heatmap cells. "haploview" uses the classic Haploview scheme where cell color is determined by both LOD score and \(D'\): LOD < 2 and \(D'\) < 1 gives white, LOD < 2 and \(D'\) = 1 gives blue, LOD \(\ge\) 2 and \(D'\) < 1 gives shades of pink/red scaled by \(D'\), and LOD \(\ge\) 2 and \(D'\) = 1 gives bright red. All other options use continuous viridis-family palettes: "viridis" (default), "magma", "inferno", "plasma", "cividis", "rocket", "mako", and "turbo".

ldBlocks

Optional specification of genomic regions to highlight as LD blocks on the plot. Accepted formats:

• A LDRegion object (single block) or a list of LDRegion objects (multiple blocks). Each region carries start, end, an optional label, and an outline color. The chromosome is inferred from the data (single-chromosome only).

• A GRanges object where each range defines a chromosome and start/end positions. An optional label metadata column (in mcols) adds text annotations. Block outlines default to black.

Sites falling within each region are outlined with a triangular border. Defaults to NULL.

genomicTrack

Logical. If TRUE, a horizontal genomic track is drawn above the LD plot showing the approximate physical positions of each site along the chromosome. Site IDs are placed at their physical positions on the track, and line segments connect each physical position to the corresponding evenly-spaced position above the LD triangle. When data span multiple chromosomes, positions are displayed cumulatively. Defaults to FALSE.

showIndex

Logical. If TRUE (default), numeric index labels (1, 2, 3, ...) are drawn along the diagonal of the LD triangle. Set to FALSE to hide them.

verbose

Display messages? Defaults to TRUE.

Value

A ggplot object.

Details

This function visualises a pre-computed LD result set. Use linkageDiseq to calculate LD first, then pass the resulting LDResults object here.

See also

linkageDiseq, LDResults