don't default alpha to face

R/simplicial-complex.R

@@ -95,8 +95,8 @@ StatSimplicialComplex <-  ggproto(
 
   required_aes = c("x", "y"),
 
-  # Alternatively, could assign fill = after_stat(dimension)
-  default_aes = aes(alpha = after_stat(face)),
+  # default_aes = aes(fill = after_stat(dimension))
+  # default_aes = aes(alpha = after_stat(face))
 
   compute_group = function(
     data, scales,
@@ -370,7 +370,7 @@ GeomSimplicialComplex <- ggproto(
     grob
   },
 
-  default_aes = aes(colour = "black", fill = "grey30", alpha = NA,
+  default_aes = aes(colour = "black", fill = "grey30", alpha = .15,
                     linewidth = 0.5, linetype = 1,
                     shape = 21L, size = 1.5, stroke = .5),
 

README.md

@@ -108,7 +108,6 @@ gridExtra::grid.arrange(
   p_d, p_sc,
   layout_matrix = matrix(c(1, 2), nrow = 1)
 )
-#> Warning: Using alpha for a discrete variable is not advised.
 ```
 
 <img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
@@ -265,7 +264,6 @@ ggplot(dg, aes(x, y)) +
   ) +
   theme_bw() +
   theme(legend.position = "none")
-#> Warning: Using alpha for a discrete variable is not advised.
 ```
 
 <img src="man/figures/README-unnamed-chunk-10-1.png" width="100%" />
@@ -298,7 +296,8 @@ ggplot(ds, aes(dataset = d)) +
   labs(x = "Birth", y = "Death", color = "Dimension", shape = "Dimension") +
   lims(x = c(0, max_prox), y = c(0, max_prox)) +
   theme_persist()
-#> Warning: Removed 2 rows containing missing values (`geom_point()`).
+#> Warning: Removed 2 rows containing missing values or values outside the scale range
+#> (`geom_point()`).
 ```
 
 <img src="man/figures/README-unnamed-chunk-11-1.png" width="100%" />

inst/examples/ex-draw-key-simplex.R

@@ -1,22 +1,22 @@
 
-# regular pentagon
-fifths <- (seq_len(5) - 1) * 2 * pi / 5
-pentagon <- data.frame(x = cos(fifths), y = sin(fifths))
-ggplot(pentagon, aes(x, y)) +
+# regular septagon
+sevenths <- (seq_len(7) - 1) * 2 * pi / 7
+septagon <- data.frame(x = cos(sevenths), y = sin(sevenths))
+ggplot(septagon, aes(x, y)) +
   geom_simplicial_complex(
-    diameter = 2, dimension_max = 5L, one_simplices = "all",
+    diameter = 1.6, dimension_max = 5L, one_simplices = "all",
     engine = "simplextree",
     aes(color = after_stat(factor(dimension)),
         fill = after_stat(factor(dimension))),
     alpha = .5
   )
 
-# regular septagon
-sevenths <- (seq_len(7) - 1) * 2 * pi / 7
-septagon <- data.frame(x = cos(sevenths), y = sin(sevenths))
-ggplot(septagon, aes(x, y)) +
+# regular pentagon
+fifths <- (seq_len(5) - 1) * 2 * pi / 5
+pentagon <- data.frame(x = cos(fifths), y = sin(fifths))
+ggplot(pentagon, aes(x, y)) +
   geom_simplicial_complex(
-    diameter = 1.6, dimension_max = 5L, one_simplices = "all",
+    diameter = 2, dimension_max = 5L, one_simplices = "all",
     engine = "simplextree",
     aes(color = after_stat(factor(dimension)),
         fill = after_stat(factor(dimension))),

inst/examples/ex-simplicial-complex.R

@@ -6,17 +6,31 @@ df <- data.frame(
   y = sin(s) + rnorm(40, 0, .1)
 )
 
-# default, visualizing dimension w/ alpha:
+# default
 ggplot(df, aes(x, y)) +
   coord_fixed() +
   geom_simplicial_complex(radius = .4)
-# visualizing dimension w/ fill:
+# higher-dimensional simplices are not more opaque but cause overlap
+ggplot(df, aes(x, y)) +
+  coord_fixed() +
+  geom_simplicial_complex(radius = .4, dimension_max = 3L)
+
+# visualizing dimension w/ face & alpha:
+ggplot(df, aes(x, y)) +
+  coord_fixed() +
+  geom_simplicial_complex(
+    mapping = aes(alpha = after_stat(face)),
+    radius = .3, dimension_max = 4L
+  ) +
+  scale_alpha_ordinal(range = c(.1, .6))
+# visualizing dimension w/ dimension & fill:
 ggplot(df, aes(x, y)) +
   coord_fixed() +
   geom_simplicial_complex(
     mapping = aes(fill = after_stat(dimension)),
-    alpha = .5, radius = .4
-  )
+    radius = .3, dimension_max = 4L, alpha = .25
+  ) +
+  scale_fill_continuous(type = "viridis")
 
 # with a zero radius or diameter
 ggplot(df, aes(x = x, y = y)) +