R/visualisation_recipe.easycormatrix.R

In correlation: Methods for Correlation Analysis

#' Visualisation Recipe for 'correlation' Objects
#'
#' Objects from the `correlation` package can be easily visualized. You can
#' simply run `plot()` on them, which will internally call the `visualisation_recipe()`
#' method to produce a basic `ggplot`. You can customize this plot ad-hoc or via
#' the arguments described below.
#' See examples [**here**](https://easystats.github.io/correlation/reference/visualisation_recipe.easycormatrix.html#ref-examples).
#'
#' @param x A correlation object.
#' @param show_text Show labels with matrix values.
#' @param show_data Show data. For correlation matrices, can be `"tile"`
#'   (default) or `"point"`.
#' @param show_legend Show legend. Can be set to `FALSE` to remove the legend.
#' @param type Alias for `show_data`, for backwards compatibility.
#' @param tile,point,text,scale,scale_fill,smooth,labs Additional aesthetics and
#'   parameters for the geoms (see customization example).
#' @param ... Other arguments passed to other functions.
#'
#' @examples
#' # ==============================================
#' # Correlation Matrix
#' # ==============================================
#' if (require("see")) {
#'   rez <- correlation(mtcars)
#'
#'   x <- cor_sort(as.matrix(rez))
#'   layers <- visualisation_recipe(x)
#'   layers
#'   plot(layers)
#'
#'   #' Get more details using `summary()`
#'   x <- summary(rez, redundant = TRUE, digits = 3)
#'   plot(visualisation_recipe(x))
#'
#'   # Customize
#'   x <- summary(rez)
#'   layers <- visualisation_recipe(x,
#'     show_data = "points",
#'     scale = list(range = c(10, 20)),
#'     scale_fill = list(
#'       high = "#FF5722",
#'       low = "#673AB7",
#'       name = "r"
#'     ),
#'     text = list(color = "white"),
#'     labs = list(title = "My Plot")
#'   )
#'   plot(layers) + theme_modern()
#' }
#' @export
visualisation_recipe.easycormatrix <- function(x,
                                               show_data = "tile",
                                               show_text = "text",
                                               show_legend = TRUE,
                                               tile = NULL,
                                               point = NULL,
                                               text = NULL,
                                               scale = NULL,
                                               scale_fill = NULL,
                                               labs = NULL,
                                               type = show_data,
                                               ...) {
  # handle alias
  if (!missing(type)) {
    show_data <- type
  }

  # process dot-arguments ------------------------------
  ellipses <- list(...)
  show_text <- !isFALSE(ellipses$show_values)
  show_p <- !isFALSE(ellipses$show_p)

  # default style for tiles
  if (is.null(tile)) {
    tile <- list(color = "white", size = 0.6)
  } else {
    if (is.null(tile$color)) {
      tile$color <- "white"
    }
    if (is.null(tile$size)) {
      tile$size <- 0.6
    }
  }

  # remember if full matrix
  is_redundant <- attributes(x)$redundant

  # Format as summary() if true matrix
  if (inherits(x, "matrix")) {
    data_text <- NULL
    x <- cbind(data.frame(Parameter1 = row.names(x)), as.data.frame(x))
  } else {
    data_text <- format(x, ...)
    names(data_text)[names(data_text) == "Parameter"] <- "Parameter1"
    names(x)[names(x) == "Parameter"] <- "Parameter1"
    x <- as.data.frame(x)
  }
  colnames <- names(x)[names(x) != "Parameter1"]

  # Reshape to long
  data <- datawizard::reshape_longer(x,
    select = colnames,
    names_to = "Parameter2",
    values_to = "r"
  )

  # Text
  if (is.null(data_text)) {
    data$Text <- paste0(insight::format_value(data$r, zap_small = TRUE))
  } else {
    temp <- datawizard::reshape_longer(data_text,
      select = colnames,
      names_to = "Parameter2",
      values_to = "Text"
    )
    data <- merge(data, temp, all.x = TRUE, all.y = FALSE)
  }

  # remove p-values
  if (!show_p) {
    data$Text <- gsub("*", "", data$Text, fixed = TRUE)
  }

  # Format
  data$Parameter1 <- factor(data$Parameter1, levels = rev(x$Parameter1))
  data$Parameter2 <- factor(data$Parameter2, levels = colnames)

  # filter `NA`s
  data <- data[!is.na(data$r), ]

  # add absolute r-value, required as aes for point size
  data$abs_r <- abs(data$r)

  # if redundant, remove diagonal self-correlation, and fill with NA again
  if (isTRUE(is_redundant)) {
    self_cor <- which(data$Parameter1 == data$Parameter2)
    data$r[self_cor] <- NA
    data$Text[self_cor] <- ""
  }

  # Initialize layers list
  layers <- list()

  # Layers -----------------------
  l <- 1

  # Add tiles
  if (!is.null(show_data)) {
    if (isTRUE(show_data) || show_data %in% c("tile", "tiles")) {
      layers[[paste0("l", l)]] <- .visualisation_easycormatrix_data(
        type = "tile",
        data, x = "Parameter2",
        y = "Parameter1",
        fill = "r",
        args = tile,
        dot_args = ellipses
      )
    } else {
      layers[[paste0("l", l)]] <- .visualisation_easycormatrix_data(
        type = "point",
        data,
        x = "Parameter2",
        y = "Parameter1",
        fill = "r",
        args = point,
        dot_args = ellipses,
        abs_fill = "abs_r"
      )
    }
    l <- l + 1
  }



  # Add text
  if (!is.null(show_text) && !isFALSE(show_text)) {
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_text(
      data,
      x = "Parameter2",
      y = "Parameter1",
      label = "Text",
      text = text
    )
    l <- l + 1
  }

  # Color tiles
  if (!is.null(show_data) && show_data %in% c("tile", "tiles")) {
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_scale_fill(
      type = "fill",
      data,
      scale_fill = scale_fill,
      show_legend = show_legend
    )
    l <- l + 1
  } else if (show_data %in% c("point", "points")) {
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_scale_fill(
      type = "colour",
      data,
      scale_fill = scale_fill,
      show_legend = show_legend
    )
    l <- l + 1
  }

  # Origin at 0
  if (!is.null(show_data) && show_data %in% c("tile", "tiles")) {
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_scale(which = "x_discrete", scale = scale)
    l <- l + 1
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_scale(which = "y_discrete", scale = scale)
    l <- l + 1
  } else if (show_data %in% c("point", "points")) {
    layers[[paste0("l", l)]] <- .visualisation_easycormatrix_scale(which = "size", scale = scale)
    l <- l + 1
  }

  # Labs
  layers[[paste0("l", l)]] <- .visualisation_easycormatrix_labs(labs)

  # Out
  class(layers) <- c("visualisation_recipe", "see_visualisation_recipe", class(layers))
  attr(layers, "data") <- data
  layers
}



# Layer - Data -------------------------------------------------------------

.visualisation_easycormatrix_data <- function(type = "tile",
                                              data,
                                              x,
                                              y,
                                              fill,
                                              args = NULL,
                                              dot_args = NULL,
                                              abs_fill = NULL) {
  out <- list(
    geom = type,
    data = data,
    aes = list(
      y = y,
      x = x
    )
  )

  if (type == "point") {
    out$aes$colour <- fill
    # point size?
    if (!is.null(dot_args$point_size)) {
      out$size <- dot_args$point_size
    } else if (!is.null(dot_args$size_point)) {
      out$size <- dot_args$size_point
    } else if (!is.null(abs_fill)) {
      # hack needed for size-aes for point-geoms
      out$aes$size <- abs_fill
    } else {
      out$aes$size <- paste0("abs(", fill, ")")
    }
    out$stroke <- 0
    out$shape <- 16
    out$show.legend <- c("size" = FALSE)
  } else {
    out$aes$fill <- fill
  }
  if (!is.null(args)) out <- utils::modifyList(out, args) # Update with additional args
  out
}



# Layer - Scale Fill -------------------------------------------------------------

.visualisation_easycormatrix_scale_fill <- function(type = "fill", data, scale_fill = NULL, show_legend = TRUE) {
  low_lim <- ifelse(min(data$r, na.rm = TRUE) < 0, -1, 0)
  high_lim <- ifelse(max(data$r, na.rm = TRUE) > 0, 1, 0)

  out <- list(
    geom = paste0("scale_", type, "_gradient2"),
    low = "#F44336",
    mid = "white",
    high = "#2196F3",
    midpoint = 0,
    na.value = "grey85",
    limit = c(low_lim, high_lim),
    space = "Lab",
    name = "Correlation",
    guide = ifelse(isFALSE(show_legend), "none", "legend")
  )
  if (!is.null(scale_fill)) out <- utils::modifyList(out, scale_fill) # Update with additional args
  out
}


# Layer - Text -------------------------------------------------------------

.visualisation_easycormatrix_text <- function(data, x, y, label, show_text = "text", text = NULL) {
  out <- list(
    geom = show_text,
    data = data,
    aes = list(
      y = y,
      x = x,
      label = label
    )
  )
  if (!is.null(text)) out <- utils::modifyList(out, text) # Update with additional args
  out
}


# Layer - Scale -------------------------------------------------------------------


.visualisation_easycormatrix_scale <- function(which = "x_discrete", scale = NULL) {
  if (which == "size") {
    out <- list(
      geom = "scale_size",
      range = c(5, 15)
    )
  } else {
    out <- list(
      geom = paste0("scale_", which),
      expand = c(0, 0)
    )
  }

  if (!is.null(scale)) out <- utils::modifyList(out, scale) # Update with additional args
  out
}


# Layer - Labs -------------------------------------------------------------------


.visualisation_easycormatrix_labs <- function(labs = NULL) {
  out <- list(
    geom = "labs",
    x = NULL,
    y = NULL,
    title = "Correlation Matrix"
  )
  if (!is.null(labs)) out <- utils::modifyList(out, labs) # Update with additional args
  out
}