Clean up appearance of shadows and make them the default

R/adjustment_sets.R

@@ -77,15 +77,15 @@ ggdag_adjustment_set <- function(
   exposure = NULL,
   outcome = NULL,
   ...,
-  shadow = FALSE,
+  shadow = TRUE,
   size = 1,
   node_size = 16,
   text_size = 3.88,
   label_size = text_size,
   text_col = "white",
   label_col = "black",
   edge_width = 0.6,
-  edge_cap = 8,
+  edge_cap = 10,
   arrow_length = 5,
   use_edges = TRUE,
   use_nodes = TRUE,
@@ -111,24 +111,21 @@ ggdag_adjustment_set <- function(
     expand_plot(expand_x = expand_x, expand_y = expand_y)
 
   if (shadow) {
-    p <- p + geom_dag_edges(
-      ggplot2::aes(edge_alpha = adjusted),
-      start_cap = ggraph::circle(10, "mm"),
-      end_cap = ggraph::circle(10, "mm")
-    )
+    vals <- c("unadjusted" = "black", "adjusted" = "grey80")
   } else {
     vals <- c("unadjusted" = "black", "adjusted" = "#FFFFFF00")
-    p <- p + geom_dag_edges(
-      ggplot2::aes(edge_colour = adjusted),
-      show.legend = FALSE
-    ) +
-      ggraph::scale_edge_colour_manual(
-        drop = FALSE,
-        values = vals,
-        limits = names(vals)
-      )
   }
 
+  p <- p + geom_dag_edges(
+    ggplot2::aes(edge_colour = adjusted),
+    show.legend = if (shadow) TRUE else FALSE
+  ) +
+    ggraph::scale_edge_colour_manual(
+      drop = FALSE,
+      values = vals,
+      limits = names(vals)
+    )
+
   p <- p +
     geom_dag(
       size = size,
@@ -266,7 +263,7 @@ ggdag_adjust <- function(
       start_cap = ggraph::circle(edge_cap, "mm"),
       end_cap = ggraph::circle(edge_cap, "mm")
     ) +
-    scale_adjusted() +
+    scale_adjusted(include_alpha = TRUE) +
     expand_plot(expand_y = expansion(c(0.2, 0.2)))
 
   if (collider_lines) p <- p + geom_dag_collider_edges()

R/colliders.R

@@ -75,8 +75,7 @@ ggdag_collider <- function(
   p <- if_not_tidy_daggity(.tdy_dag, ...) %>%
     node_collider() %>%
     dplyr::mutate(colliders = forcats::fct_rev(colliders)) %>%
-    ggplot2::ggplot(aes_dag(color = colliders)) +
-    scale_adjusted()
+    ggplot2::ggplot(aes_dag(color = colliders))
 
   p <- p + geom_dag(
     size = size,

R/geom_dag.R

@@ -980,6 +980,7 @@ aes_dag <- function(...) {
 #' you'll find that it is awkward for sophisticated customization. When you hit
 #' that point, you should use the underlying geoms directly.
 #'
+#' @inheritParams ggplot2::geom_point
 #' @param size A numeric value scaling the size of all elements in the DAG. This
 #'   allows you to change the scale of the DAG without changing the proportions.
 #' @param edge_type The type of edge, one of "link_arc", "link", "arc",
@@ -1021,6 +1022,7 @@ aes_dag <- function(...) {
 #'
 #' @export
 geom_dag <- function(
+  data = NULL,
   size = 1,
   edge_type = c("link_arc", "link", "arc", "diagonal"),
   node_size = 16,
@@ -1073,6 +1075,7 @@ geom_dag <- function(
           start_cap = ggraph::circle(sizes[["cap"]], "mm"),
           end_cap = ggraph::circle(sizes[["cap"]], "mm")
         ),
+        data = data,
         edge_width = sizes[["edge"]],
         arrow = grid::arrow(length = grid::unit(sizes[["arrow"]], "pt"), type = "closed")
       )
@@ -1083,9 +1086,9 @@ geom_dag <- function(
 
   if (isTRUE(use_nodes)) {
     if (isTRUE(use_stylized)) {
-      node_geom <- geom_dag_node(size = sizes[["node"]])
+      node_geom <- geom_dag_node(size = sizes[["node"]], data = data)
     } else {
-      node_geom <- geom_dag_point(size = sizes[["node"]])
+      node_geom <- geom_dag_point(size = sizes[["node"]], data = data)
     }
   } else {
     node_geom <- NULL
@@ -1117,7 +1120,12 @@ geom_dag <- function(
       mapping <- NULL
     }
 
-    text_geom <- geom_dag_text(mapping = mapping, col = text_col, size = text_size)
+    text_geom <- geom_dag_text(
+      mapping = mapping,
+      data = data,
+      col = text_col,
+      size = text_size
+    )
   } else {
     text_geom <- NULL
   }
@@ -1151,6 +1159,7 @@ geom_dag <- function(
 
     label_geom <- geom_dag_label_repel(
       ggplot2::aes(label = !!label),
+      data = data,
       size = sizes[["label"]] * 1.1,
       col = label_col,
       show.legend = FALSE,

R/paths.R

@@ -17,8 +17,7 @@
 #' @param paths_only logical. Should only open paths be returned? Default is
 #'   `FALSE`, which includes every variable and edge in the DAG regardless
 #'   if they are part of the path.
-#' @param shadow logical. Show edges which are not on an open path? Ignored if
-#'   `paths_only` is `TRUE`.
+#' @param shadow logical. Show edges which are not on an open path?
 #' @param ... additional arguments passed to `tidy_dagitty()`
 #' @inheritParams geom_dag
 #' @param spread the width of the fan spread
@@ -112,7 +111,7 @@ ggdag_paths <- function(
   adjust_for = NULL,
   limit = 100,
   directed = FALSE,
-  shadow = FALSE,
+  shadow = TRUE,
   ...,
   size = 1,
   edge_type = c("link_arc", "link", "arc", "diagonal"),
@@ -135,21 +134,42 @@ ggdag_paths <- function(
   stylized = deprecated()
 ) {
   p <- if_not_tidy_daggity(.tdy_dag, ...) %>%
-    dag_paths(from = from, to = to, adjust_for = adjust_for, limit = limit, directed = directed, paths_only = !shadow) %>%
-    ggplot2::ggplot(aes_dag(col = path, alpha = path)) +
-    geom_dag_edges(ggplot2::aes(edge_alpha = path, edge_colour = path)) +
+    dag_paths(from = from, to = to, adjust_for = adjust_for, limit = limit, directed = directed) %>%
+    ggplot2::ggplot(aes_dag(color = path)) +
+    geom_dag_edges(
+      ggplot2::aes(edge_colour = path),
+      show.legend = if (shadow) TRUE else FALSE
+    ) +
     ggplot2::facet_wrap(~ forcats::fct_inorder(as.factor(set))) +
-    ggplot2::scale_alpha_manual(drop = FALSE, values = c("open path" = 1), na.value = .35, breaks = "open path", limits = "open path") +
-    ggraph::scale_edge_alpha_manual(drop = FALSE, values = c("open path" = 1), na.value = .35, breaks = "open path", limits = "open path") +
-    ggraph::scale_edge_colour_discrete(drop = FALSE, breaks = "open path") +
-    ggplot2::scale_color_discrete(drop = FALSE, breaks = "open path") +
+    breaks("open path") +
     expand_plot(
       expand_x = expansion(c(0.25, 0.25)),
       expand_y = expansion(c(0.1, 0.1))
     )
 
+  if (shadow) {
+    vals <- c("unadjusted" = "black", "adjusted" = "grey80")
+  } else {
+    vals <- c("unadjusted" = "black", "adjusted" = "#FFFFFF00")
+  }
+
+  p <- p +
+    ggraph::scale_edge_color_discrete(
+      drop = FALSE,
+      na.value = if (shadow) "grey80" else "#FFFFFF00",
+      na.translate = if (shadow) TRUE else FALSE,
+      limits = "open path"
+    ) +
+    ggplot2::scale_color_discrete(
+      drop = FALSE,
+      na.value = if (shadow) "grey80" else "#FFFFFF00",
+      na.translate = if (shadow) TRUE else FALSE,
+      limits = "open path"
+    )
+
   p <- p +
     geom_dag(
+      data = if (!shadow) function(x) dplyr::filter(x, path == "open path"),
       size = size,
       node_size = node_size,
       text_size = text_size,
@@ -183,7 +203,7 @@ ggdag_paths_fan <- function(
   limit = 100,
   directed = FALSE,
   ...,
-  shadow = FALSE,
+  shadow = TRUE,
   spread = .7,
   size = 1,
   node_size = 16,

R/themes.R

@@ -120,6 +120,7 @@ theme_dag_gray_grid <- theme_dag_grey_grid
 #' whenever [geom_dag_collider_edges()] is used. `scale_dag()` is deprecated in
 #' favor of `scale_adjusted()`.
 #'
+#' @param include_alpha Logical. Include alpha-related scales?
 #' @param breaks One of:
 #'
 #'   - NULL for no breaks
@@ -133,12 +134,13 @@ theme_dag_gray_grid <- theme_dag_grey_grid
 #'
 #' @export
 #' @rdname scale_adjusted
-scale_adjusted <- function() {
+scale_adjusted <- function(include_alpha = FALSE) {
   list(
     ggplot2::scale_linetype_manual(name = NULL, values = "dashed"),
     ggplot2::scale_shape_manual(drop = FALSE, values = c("adjusted" = 15, "unadjusted" = 19), limits = c("adjusted", "unadjusted")),
-    ggplot2::scale_alpha_manual(drop = FALSE, values = c("adjusted" = .30, "unadjusted" = 1), limits = c("adjusted", "unadjusted")),
-    ggraph::scale_edge_alpha_manual(name = NULL, drop = FALSE, values = c("adjusted" = .30, "unadjusted" = 1), limits = c("adjusted", "unadjusted"))
+    ggplot2::scale_color_discrete(limits = c("adjusted", "unadjusted")),
+    if (include_alpha) ggplot2::scale_alpha_manual(drop = FALSE, values = c("adjusted" = .30, "unadjusted" = 1), limits = c("adjusted", "unadjusted")),
+    if (include_alpha) ggraph::scale_edge_alpha_manual(name = NULL, drop = FALSE, values = c("adjusted" = .30, "unadjusted" = 1), limits = c("adjusted", "unadjusted"))
   )
 }