mdir (version 0.9.0)

prepSimilarityMatricesForGGplot: Prepare similarity matrices for ggplot

Description

Given a list of symmatric similarity matrices, converts them to the correct formatting for ggplot2, optionally giving all a common ordering.

Usage

prepSimilarityMatricesForGGplot(
  similarity_matrices,
  matrix_setting_order = 1,
  use_common_ordering = TRUE,
  ignore_checks = TRUE,
  y_axis = "y",
  x_axis = "x"
)

Value

A long data.frame containing columns `x` (the x-axis position of the entry for geom_tile()), `y` (the y-axis position of the entry for geom_tile()), `Entry` (value in similarity matrix) and `Chain` (assumes chains are ordered from one to the number of chains present).

Arguments

similarity_matrices

List of similarity matrices

matrix_setting_order

The matrix that defines the ordering of all others, if a common ordering is used. Defaults to `1`.

use_common_ordering

Logical indicating if a common ordering should be used. If false all matrices are ordered individually, defaults to `TRUE`.

ignore_checks

Logical indicating if checks for matrix symmetry and a commmon size should be ignored. Defaults to TRUE as these checks seem to break when they should not.

y_axis

The name for the column defining the y-axis. Defaults to ``"y"``.

x_axis

The name for the column defining the x-axis. Defaults to ``"x"``.

Examples

# \donttest{
N <- 100
X <- matrix(c(rnorm(N, 0, 1), rnorm(N, 3, 1)), ncol = 2, byrow = TRUE)
Y <- matrix(c(rnorm(N, 0, 1), rnorm(N, 3, 1)), ncol = 2, byrow = TRUE)

truth <- c(rep(1, N / 2), rep(2, N / 2))
data_modelled <- list(X, Y)

V <- length(data_modelled)

# MCMC parameters
R <- 5000
thin <- 50
burn <- 1000

K_max <- 10
K <- rep(K_max, V)
types <- rep("G", V)

n_chains <- 3
mcmc_out <- runMCMCChains(data_modelled, n_chains, R, thin, types, K = K)
mcmc_out <- processMCMCChains(mcmc_out, burn, construct_psm = TRUE)

psms_v1 <- list()
for (ii in seq(1, n_chains)) {
  psms_v1[[ii]] <- mcmc_out[[ii]]$psms[[1]]
}

plot_df <- prepSimilarityMatricesForGGplot(psms_v1)
plot_df |>
  ggplot2::ggplot(ggplot2::aes(x = x, y = y, fill = Entry)) +
  ggplot2::geom_tile() +
  ggplot2::facet_wrap(~Chain) +
  ggplot2::scale_fill_gradient(low = "#FFFFFF", high = "#146EB4")
# }