vismat: Visualize Relationship Matrices

In visPedigree: Tidying, Analysis, and Fast Visualization of Animal and Plant Pedigrees

Visualize Relationship Matrices

Description

vismat provides visualization tools for relationship matrices (A, D, AA), supporting individual-level heatmaps and relationship coefficient histograms. This function is useful for exploring population genetic structure, identifying inbred individuals, and analyzing kinship between families.

Usage

vismat(
  mat,
  ped = NULL,
  type = "heatmap",
  ids = NULL,
  reorder = TRUE,
  by = NULL,
  grouping = NULL,
  labelcex = NULL,
  ...
)

Arguments

mat	A relationship matrix. Can be one of the following types: A pedmat object returned by pedmat — including compact matrices. When by is specified, group-level means are computed directly from the compact matrix (no full expansion needed). Without by, compact matrices are automatically expanded to full dimensions before plotting (see Details). A tidyped object (automatically calculates additive relationship matrix A). A named list containing matrices (preferring A, D, AA). A standard matrix or Matrix object. Note: Inverse matrices (Ainv, Dinv, AAinv) are not supported for visualization because their elements do not represent meaningful relationship coefficients.
ped	Optional. A tidied pedigree object (tidyped), used for extracting labels or grouping information. Required when using the by parameter with a plain matrix input. If mat is a pedmat object, the pedigree is extracted automatically.
type	Character, type of visualization. Supported options: "heatmap": Relationship matrix heatmap (default). Uses a Nature Genetics style color palette (white-orange-red-dark red), with optional hierarchical clustering and group aggregation. "histogram": Distribution histogram of relationship coefficients. Shows the frequency distribution of lower triangular elements (pairwise kinship).
ids	Character vector specifying individual IDs to display. Used to filter and display a submatrix of specific individuals. If NULL (default), all individuals are shown.
reorder	Logical. If TRUE (default), rows and columns are reordered using hierarchical clustering (Ward.D2 method) to bring closely related individuals together. Only affects heatmap visualization. Automatically skipped for large matrices (N > VISMAT_REORDER_MAX, default 2 000) to improve performance. Clustering principle: Based on relationship profile distance (Euclidean distance between rows). Full-sibs have nearly identical relationship profiles with the whole population, so they cluster tightly together and appear as contiguous blocks in the heatmap.
by	Optional. Column name in ped to group by (e.g., "Family", "Gen", "Year"). When grouping is enabled: Individual-level matrix is aggregated to a group-level matrix (computing mean relationship coefficients between groups). For "Family" grouping, founders without family assignment are excluded. For other grouping columns, NA values are assigned to an "Unknown" group. Useful for visualizing population structure in large pedigrees.
grouping	[Deprecated] Use by instead.
labelcex	Numeric. Manual control for font size of individual labels. If NULL (default), uses a dynamic font size that adjusts automatically based on matrix dimensions (range 0.2–0.7). Labels are hidden automatically when N > VISMAT_LABEL_MAX (default 500).
...	Additional arguments passed to the underlying plotting function: Heatmap uses levelplot: can set main, xlab, ylab, col.regions, colorkey, scales, etc. Histogram uses histogram: can set main, xlab, ylab, nint (number of bins), etc.

Details

Compact Matrix Handling

When mat is a compact pedmat object (created with pedmat(..., compact = TRUE)):

• With by: Group-level mean relationships are computed algebraically from the K×K compact matrix, including a correction for sibling off-diagonal values. This avoids expanding to the full N×N matrix, making family-level or generation-level visualization feasible even for pedigrees with hundreds of thousands of individuals.

• Without by, N > VISMAT_EXPAND_MAX (5 000): The compact K\timesK matrix is plotted directly using representative individuals. Labels show the number of individuals each representative stands for, e.g., "ID (\u00d7350)". This avoids memory-intensive full expansion.

• Without by, N \le 5 000: The compact matrix is expanded via expand_pedmat to restore full dimensions.

Heatmap

• Uses a Nature Genetics style color palette (white to orange to red to dark red).

• Hierarchical clustering reordering (Ward.D2) is enabled by default.

• Grid lines shown when N \le VISMAT_GRID_MAX (100); labels shown when N \le VISMAT_LABEL_MAX (500).

• mat[1,1] is displayed at the top-left corner.

Histogram

• Shows the distribution of lower-triangular elements (pairwise kinship).

• X-axis: relationship coefficient values; Y-axis: frequency percentage.

Performance

The following automatic thresholds are defined as package-internal constants (VISMAT_*) at the top of R/vismat.R:

• VISMAT_EXPAND_MAX (5 000): compact matrices with original N above this are shown in representative view instead of expanding.

• VISMAT_REORDER_MAX (2 000): hierarchical clustering is automatically skipped.

• VISMAT_LABEL_MAX (500): individual labels are hidden.

• VISMAT_GRID_MAX (100): cell grid lines are hidden.

• by grouping uses vectorized rowsum() algebra — suitable for large matrices.

Interpreting Relationship Coefficients

For the additive relationship matrix A:

• Diagonal elements = 1 + F (F = inbreeding coefficient).

• Off-diagonal elements = 2 × kinship coefficient.

• 0: unrelated; 0.25: half-sibs / grandparent–grandchild; 0.5: full-sibs / parent–offspring; 1.0: same individual.

Value

Invisibly returns the lattice plot object. The plot is rendered on the current graphics device.

See Also

pedmat for computing relationship matrices, expand_pedmat for manually restoring compact matrix dimensions, query_relationship for querying individual pairs, tidyped for tidying pedigree data, visped for visualizing pedigree structure graphs, levelplot, histogram

Examples

library(visPedigree)
data(small_ped)
ped <- tidyped(small_ped)

# ============================================================
# Basic Usage
# ============================================================

# Method 1: from tidyped object (auto-computes A)
vismat(ped)

# Method 2: from pedmat object
A <- pedmat(ped)
vismat(A)

# Method 3: from plain matrix
vismat(as.matrix(A))

# ============================================================
# Compact Pedigree (auto-expanded before plotting)
# ============================================================

# For pedigrees with large full-sib families, compute a compact matrix
# first for efficiency, then pass directly to vismat() — it automatically
# expands back to full dimensions.
A_compact <- pedmat(ped, compact = TRUE)
vismat(A_compact)   # prints: "Expanding compact matrix (N -> M individuals)"

# For very large pedigrees, aggregate to a group-level view instead
vismat(A, ped = ped, by = "Gen",
       main = "Mean Relationship Between Generations")

# ============================================================
# Heatmap Customization
# ============================================================

# Custom title and axis labels
vismat(A, main = "Additive Relationship Matrix",
       xlab = "Individual", ylab = "Individual")

# Preserve original pedigree order (no clustering)
vismat(A, reorder = FALSE)

# Custom label font size
vismat(A, labelcex = 0.5)

# Custom color palette (blue-white-red)
vismat(A, col.regions = colorRampPalette(c("blue", "white", "red"))(100))

# ============================================================
# Display a Subset of Individuals
# ============================================================

target_ids <- rownames(A)[1:8]
vismat(A, ids = target_ids)

# ============================================================
# Histogram of Relationship Coefficients
# ============================================================

vismat(A, type = "histogram")
vismat(A, type = "histogram", nint = 30)

# ============================================================
# Group-level Aggregation
# ============================================================

# Group by generation
vismat(A, ped = ped, by = "Gen",
       main = "Mean Relationship Between Generations")

# Group by full-sib family (founders without a family are excluded)
vismat(A, ped = ped, by = "Family")

# ============================================================
# Other Relationship Matrices
# ============================================================

# Dominance relationship matrix
D <- pedmat(ped, method = "D")
vismat(D, main = "Dominance Relationship Matrix")

visPedigree documentation built on March 30, 2026, 9:07 a.m.