Added bin_contours argument to moranPlot

R/plot-univar-downstream.R

@@ -1,6 +1,6 @@
 .moran_ggplot <- function(mp, feature, is_singleton, contour_color = "cyan",
  color_by = NULL, plot_singletons = TRUE,
- divergent = FALSE, diverge_center = NULL, ...) {
+ divergent = FALSE, diverge_center = NULL, bins = NULL, ...) {
  if (!plot_singletons) {
  mp <- mp[!is_singleton, ]
  }
@@ -30,7 +30,7 @@
  # stat_density2d doesn't work when there're too few points
  # Unlikely in real data, but just in case
  # The error doesn't show up until the plot is built.
- p_test <- tryCatch(ggplot_build(p + stat_density2d(...)),
+ p_test <- tryCatch(ggplot_build(p + stat_density2d(bins = bins, ...)),
  error = function(e) {
  warning("Too few points for stat_density2d, not plotting contours.")
  },
@@ -39,7 +39,7 @@
  }
  )
  if (is(p_test, "ggplot_built")) {
- p <- p + geom_density2d(color = contour_color, ...)
+ p <- p + geom_density2d(color = contour_color, bins = bins, ...)
  }
  p <- p +
  geom_smooth(formula = y ~ x, method = "lm") +
@@ -102,13 +102,13 @@
 
 .moran_ggplot_filled <- function(mp, feature, is_singleton, color_by = NULL,
  plot_singletons = TRUE, divergent = FALSE,
- diverge_center = NULL, ...) {
+ diverge_center = NULL, bins = NULL, ...) {
  if (!plot_singletons) {
  mp <- mp[!is_singleton, ]
  }
  x <- wx <- is_inf <- NULL
  p <- ggplot(mp, aes(x = x, y = wx)) +
- geom_density2d_filled(show.legend = FALSE, ...)
+ geom_density2d_filled(show.legend = FALSE, bins = bins, ...)
  if (plot_singletons) {
  p <- p +
  geom_point(
@@ -143,7 +143,9 @@
  x = feature,
  y = paste("Spatially lagged", feature),
  shape = "Influential"
- )
+ ) +
+ theme(panel.background = element_rect(fill = scales::viridis_pal(option = "E")(255)[1]),
+ panel.grid = element_blank())
 }
 
 #' Use ggplot to plot the moran.plot results
@@ -185,6 +187,8 @@
 #' different palette if \code{binned = TRUE}.
 #' @param name Name under which the Moran plot results are stored. By default
 #' "moran.plot".
+#' @param bins_contour Number of bins in the point density contour. Use a
+#' smaller number to make sparser contours.
 #' @param ... Other arguments to pass to \code{\link{geom_density2d}}.
 #' @return A ggplot object.
 #' @importFrom ggplot2 geom_point geom_smooth geom_hline geom_vline
@@ -216,7 +220,8 @@ moranPlot <- function(sfe, feature, graphName = 1L, sample_id = "all",
  filled = FALSE, divergent = FALSE, diverge_center = NULL,
  swap_rownames = NULL, show_symbol = deprecated(),
  bins = 100, binwidth = NULL, hex = FALSE,
- plot_influential = TRUE, name = "moran.plot", ...) {
+ plot_influential = TRUE, bins_contour = NULL,
+ name = "moran.plot", ...) {
  l <- .deprecate_show_symbol("moranPlot", show_symbol, swap_rownames)
  show_symbol <- l[[1]]; swap_rownames <- l[[2]]
 
@@ -280,12 +285,12 @@ moranPlot <- function(sfe, feature, graphName = 1L, sample_id = "all",
  } else if (filled) {
  .moran_ggplot_filled(
  mp, feature, is_singleton, color_by, plot_singletons,
- divergent, diverge_center, ...
+ divergent, diverge_center, bins = bins_contour, ...
  )
  } else {
  .moran_ggplot(
  mp, feature, is_singleton, contour_color, color_by, plot_singletons,
- divergent, diverge_center, ...
+ divergent, diverge_center, bins = bins_contour, ...
  )
  }
 }