Merge pull request #224 from stan-dev/ridgeline-size

allow changing size of ridgelines

Author: jgabry

NEWS.md

@@ -4,14 +4,17 @@
 
 * `mcmc_*()` functions now support all draws formats from the **posterior** package. (#277, @Ozan147)
 
-* `mcmc_dens()` and `mcmc_dens_overlay()` gain arguments for controlling the 
+* `mcmc_dens()` and `mcmc_dens_overlay()` gain arguments for controlling the
   the density calculation. (#258)
-  
+
 * `mcmc_hist()` and `mcmc_dens()` gain argument `alpha` for controlling transparency. (#244)
 
+* `mcmc_areas()` and `mcmc_areas_ridges()` gain an argument `border_size` for
+controlling the thickness of the ridgelines. (#224)
+
 # bayesplot 1.8.1
 
-* Fix R cmd check error on linux for CRAN 
+* Fix R cmd check error on linux for CRAN
 
 # bayesplot 1.8.0
 
@@ -32,16 +35,16 @@
 * New plotting function `ppc_km_overlay()` for outcome variables that are   
   right-censored. Empirical CCDF estimates of `yrep` are compared with the
   Kaplan-Meier estimate of `y`. (#233, #234, @fweber144)
-  
+
 * `ppc_loo_pit_overlay()` now uses a boundary correction for an improved kernel
   density estimation. The new argument `boundary_correction` defaults to TRUE but
   can be set to FALSE to recover the old version of the plot. (#171, #235,
   @ecoronado92)
-  
+
 * CmdStanMCMC objects (from CmdStanR) can now be used with extractor
   functions `nuts_params()`, `log_posterior()`, `rhat()`, and
   `neff_ratio()`. (#227)
-  
+
 * On the y axis, `ppc_loo_pit_qq(..., compare = "normal")` now plots standard
   normal quantiles calculated from the PIT values (instead of the standardized
   PIT values). (#240, #243, @fweber144)

R/mcmc-intervals.R

@@ -79,7 +79,8 @@
 #'    pars = c("alpha", "beta[4]"),
 #'    prob = 2/3,
 #'    prob_outer = 0.9,
-#'    point_est = "mean"
+#'    point_est = "mean",
+#'    border_size = 1.5 # make the ridgelines fatter
 #' )
 #' plot(p)
 #'
@@ -176,7 +177,7 @@
 #' # Example of hierarchically related parameters
 #' # plotted with ridgelines
 #' m <- shinystan::eight_schools@posterior_sample
-#' mcmc_areas_ridges(m, pars = "mu", regex_pars = "theta") +
+#' mcmc_areas_ridges(m, pars = "mu", regex_pars = "theta", border_size = 0.75) +
 #'   ggtitle("Treatment effect on eight schools (Rubin, 1981)")
 #' }
 #'
@@ -281,6 +282,8 @@ mcmc_intervals <- function(x,
 
 #' @rdname MCMC-intervals
 #' @export
+#' @param border_size For `mcmc_areas()` and `mcmc_areas_ridges()`, the size of
+#'   the ridgelines.
 mcmc_areas <- function(x,
                        pars = character(),
                        regex_pars = character(),
@@ -291,6 +294,7 @@ mcmc_areas <- function(x,
                        prob_outer = 1,
                        point_est = c("median", "mean", "none"),
                        rhat = numeric(),
+                       border_size = NULL,
                        bw = NULL,
                        adjust = NULL,
                        kernel = NULL,
@@ -371,6 +375,12 @@ mcmc_areas <- function(x,
     fill = NA
   )
 
+  if (!is.null(border_size)) {
+    args_bottom$size <- border_size
+    args_outer$size <- border_size
+    args_inner$size <- border_size
+  }
+
   if (color_by_rhat) {
     args_bottom$mapping <- args_bottom$mapping %>%
       modify_aes_(color = ~ rhat_rating)
@@ -432,8 +442,8 @@ mcmc_areas <- function(x,
     scale_y_discrete(
       limits = unique(rev(data$parameter)),
       expand = expansion(
-        add = c(0, .5 + 1/(2 * nlevels(data$parameter))),
-        mult = c(.1, .1)
+        add = c(0, 0.5 + 1/(2 * nlevels(data$parameter))),
+        mult = c(0.05, 1/(2 * nlevels(data$parameter)))
       )
     ) +
     xlim(x_lim) +
@@ -454,6 +464,7 @@ mcmc_areas_ridges <- function(x,
                              ...,
                              prob_outer = 1,
                              prob = 1,
+                             border_size = NULL,
                              bw = NULL, adjust = NULL, kernel = NULL,
                              n_dens = NULL) {
   check_ignored_arguments(...)
@@ -484,6 +495,9 @@ mcmc_areas_ridges <- function(x,
     fill = NA,
     stat = "identity"
   )
+  if (!is.null(border_size)) {
+    args_outer$size <- border_size
+  }
 
   layer_outer <- do.call(ggridges::geom_density_ridges, args_outer)
 
@@ -522,14 +536,21 @@ mcmc_areas_ridges <- function(x,
         scale = scale,
         stat = "identity")
 
+    if (!is.null(border_size)) {
+      args_inner$size <- border_size
+    }
+
     layer_list_inner[[par_num]] <- do.call(ggridges::geom_ridgeline, args_inner)
   }
 
   ggplot(datas$outer) +
     aes_(x = ~ x, y = ~ parameter) +
     layer_outer +
     scale_y_discrete(limits = unique(rev(data$parameter)),
-                     expand = c(0.05, .6)) +
+                     expand = expansion(
+                       add = c(0, 1.4 + 1/(2 * nlevels(data$parameter))),
+                       mult = c(0.05, 1/(2 * nlevels(data$parameter)))
+                     )) +
     layer_list_inner +
     layer_vertical_line +
     scale_fill_identity() +