R/path-dist.r

In tourr: Tour Methods for Multivariate Data Visualisation

#' Compute distance matrix from bases.
#'
#' @param history history of the plots
#' @export
#' @examples
#' # This code is to be used as an example but you should increase
#' # the max from 2 to 50, say, to check tour coverage.
#' flea_std <- apply(flea[,1:6], 2, function(x) (x-mean(x))/sd(x))
#' grand <- interpolate(save_history(flea_std, max = 2), 0.2)
#' # The grand tour  -----------------------------
#' # Look at the tour path in a tour, how well does it cover a sphere
#' # Using MDS to summarise the high-d space of projections
#' # Last basis is a duplicate, needs removing
#' d <- path_dist(grand[,,-dim(grand)[[3]]])
#' ord <- as.data.frame(MASS::isoMDS(d)$points)
#' require(ggplot2)
#' ggplot(data = ord, aes(x=V1, y=V2)) +
#'   geom_path() +
#'   coord_equal() +
#'   labs(x = NULL, y = NULL)
#'
#' # Compare five guided tours  -----------------------------
#' holes1d <- guided_tour(holes(), 1)
#' tour_reps <- replicate(5, save_history(flea_std, holes1d, max = 2),
#'   simplify = FALSE
#' )
#' tour_reps2 <- lapply(tour_reps, interpolate, 0.2)
#'
#' bases <- unlist(lapply(tour_reps2, as.list), recursive = FALSE)
#' class(bases) <- "history_list"
#' index_values <- paths_index(tour_reps2, holes())
#' index_values$step <- index_values$step.1
#' d <- path_dist(bases)
#' ord <- as.data.frame(cmdscale(d, 2))
#'
#' info <- cbind(ord, index_values)
#' ggplot(data = info, aes(x = step, y = value, group = try)) +
#'   geom_line()
#' ##ggplot(data = info, aes(x = V1, y = V2, group = try)) +
#' ##  geom_path() +
#' ##  geom_point(aes(size = value)) +
#' ##  coord_equal()
#' ##last_plot() + facet_wrap(~try)
path_dist <- function(history) {
  history <- as.array(history)
  n <- dim(history)[3]
  d <- matrix(NA, nrow = n, ncol = n)

  for (i in seq_len(n)) {
    for (j in seq_len(i - 1)) {
      d[i, j] <- proj_dist(history[[i]], history[[j]])
    }
  }
  stats::as.dist(d)
}