plot_matrix: Graphics for matrices

In FieldSimR: Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials

Graphics for matrices

Description

Creates a heatmap of a symmetric matrix (e.g., correlation or covariance matrix).

Usage

plot_matrix(mat, order = FALSE, group.df = NULL, labels = TRUE)

Arguments

mat	A symmetric matrix.
order	When TRUE (default is FALSE), the function agnes of the R package 'cluster' is used with default arguments to order the matrix based on a dendrogram.
group.df	An optional data frame with columns containing the variable names followed by the group numbers. When supplied, the heatmap is split into groups and then ordered (when order = TRUE).
labels	When TRUE (default), variable labels are displayed.

Value

A heatmap with x- and y-axes displaying the variable numbers, and colour gradient ranging from blue (low value) to red (high value).

Examples

# Display a random correlation matrix.

cor_mat <- rand_cor_mat(
  n = 10,
  min.cor = -1,
  max.cor = 1
)

# Define groups.
group_df <- data.frame(variable = 1:10, group = c(1, 1, 1, 1, 2, 2, 2, 3, 3, 4))

plot_matrix(
  mat = cor_mat,
  group.df = group_df,
  order = TRUE,
  labels = TRUE
)

FieldSimR documentation built on Sept. 11, 2024, 6:39 p.m.