Fix examples and checks

R/geom_swim_marker.R

@@ -9,20 +9,23 @@
 #' @inheritParams ggplot2::geom_text
 #'
 #' @examples
+#' \dontrun{
 #' all_events <- dplyr::bind_rows(
 #'   infusion_events,
 #'   end_study_events
 #' )
 #'
-#' ggplot() +
-#'   geom_swim_lane(data = patient_data,
-#'                  aes(x = start_time, xend = end_time, y = pt_id, colour = disease_assessment)) +
+#' ggplot2::ggplot() +
+#'   geom_swim_lane(
+#'     data = patient_data,
+#'     aes(x = start_time, xend = end_time, y = pt_id, colour = disease_assessment)
+#'   ) +
 #'   geom_swim_marker(
 #'     data = all_events,
 #'     aes(x = time_from_initial_infusion, y = pt_id, marker = label),
 #'     size = 10
 #'   )
-#'
+#'}
 #'
 #' @export
 

R/scale_marker.R

@@ -13,32 +13,29 @@
 #' @inheritParams ggplot2::discrete_scale
 #'
 #' @examples
-#'
+#' \dontrun{
 #' all_events <- dplyr::bind_rows(
 #'   infusion_events,
 #'   end_study_events
 #' )
 #'
-#' ggplot() +
-#'  geom_swim_marker(
-#'    data = all_events,
-#'    aes(x = time_from_initial_infusion, y = pt_id, marker = label),
-#'    size = 5
-#'  ) +
-#'  scale_marker_discrete(glyphs = all_events$glyph,
-#'                        colours = all_events$colour,
-#'                        limits = all_events$label)
+#' ggplot2::ggplot() +
+#'   geom_swim_marker(
+#'     data = all_events,
+#'     aes(x = time_from_initial_infusion, y = pt_id, marker = label),
+#'     size = 5
+#'   ) +
+#'   scale_marker_discrete(
+#'     glyphs = all_events$glyph,
+#'     colours = all_events$colour,
+#'     limits = all_events$label
+#'   )
+#'}
 #'
 #' @export
 
 scale_marker_discrete <- function(glyphs = NULL, colours = NULL, limits = NULL, ...) {
-  n_values <- max(length(glyphs), length(colours))
-
-  markers <- data.frame(
-    colours = rep(colours %||% .default_colours, length.out = n_values),
-    glyphs = rep(glyphs %||% .default_glyphs, length.out = n_values),
-    labels = limits
-  ) |>
+  markers <- data.frame(glyphs = glyphs, colours = colours, labels = limits) |>
     distinct()
 
   palette <- pal_markers(
@@ -48,8 +45,8 @@ scale_marker_discrete <- function(glyphs = NULL, colours = NULL, limits = NULL,
   )
 
   discrete_scale("marker", rlang::missing_arg(),
-                 palette = palette,
-                 limits = markers$labels, ..., na.translate = FALSE
+    palette = palette,
+    limits = markers$labels, ..., na.translate = FALSE
   )
 }
 

R/theme_ggswim.R

@@ -19,16 +19,16 @@
 #'
 #' @examples
 #' p <- ggplot2::ggplot() +
-#' geom_swim_lane(
-#'   data = patient_data,
-#'   mapping = aes(
-#'     x = start_time,
-#'     xend = end_time,
-#'     y = pt_id,
-#'     colour = disease_assessment
-#'   ),
-#'   linewidth = 3
-#' )
+#'   geom_swim_lane(
+#'     data = patient_data,
+#'     mapping = aes(
+#'       x = start_time,
+#'       xend = end_time,
+#'       y = pt_id,
+#'       colour = disease_assessment
+#'     ),
+#'     linewidth = 3
+#'   )
 #'
 #' p +
 #'   theme_ggswim()
@@ -47,7 +47,7 @@ theme_ggswim <- function(base_size = 12, base_family = "") {
 
       # Axis text
       axis.text = element_text(size = 10, face = "bold", colour = "#0D2C54"),
-      axis.text.x = element_text(margin = margin(t =10)),
+      axis.text.x = element_text(margin = margin(t = 10)),
       axis.text.y = element_text(margin = margin(r = 10)),
 
       # Axis titles
@@ -56,7 +56,7 @@ theme_ggswim <- function(base_size = 12, base_family = "") {
       axis.title.y = element_text(size = 14, face = "bold", margin = margin(r = 10)),
 
       # Axis tick marks
-      axis.ticks = element_line(size = 0.75, colour = "steelblue"),
+      axis.ticks = element_line(linewidth = 0.75, colour = "steelblue"),
       axis.ticks.length = unit(0.3, "cm"),
 
       # Legend
@@ -85,37 +85,37 @@ theme_ggswim_dark <- function(base_size = 12, base_family = "") {
   theme_minimal(base_size = base_size, base_family = base_family) +
     theme(
       # Background
-      plot.background = element_rect(fill = "#232234", color = NA),  # Dark blue background
-      panel.background = element_rect(fill = "#232234", color = NA),  # Dark blue panel background
+      plot.background = element_rect(fill = "#232234", color = NA),
+      panel.background = element_rect(fill = "#232234", color = NA),
 
       # Title and subtitle
-      plot.title = element_text(size = 18, face = "bold", hjust = 0, margin = margin(b = 10), colour = "#FE9000"),  # Orange title
-      plot.subtitle = element_text(size = 14, face = "bold", hjust = 0, margin = margin(b = 10), colour = "#D67A00"),  # Light orange subtitle
+      plot.title = element_text(size = 18, face = "bold", hjust = 0, margin = margin(b = 10), colour = "#FE9000"),
+      plot.subtitle = element_text(size = 14, face = "bold", hjust = 0, margin = margin(b = 10), colour = "#D67A00"),
 
       # Caption
-      plot.caption = element_text(size = 10, hjust = 1, colour = "#F0F0F0"),  # Light caption text
+      plot.caption = element_text(size = 10, hjust = 1, colour = "#F0F0F0"),
 
       # Axis text
-      axis.text = element_text(size = 10, face = "bold", colour = "#F0F0F0"),  # Light gray axis text
-      axis.text.x = element_text(margin = margin(t = 10), colour = "#F0F0F0"),  # Light gray axis text for x-axis
-      axis.text.y = element_text(margin = margin(r = 10), colour = "#F0F0F0"),  # Light gray axis text for y-axis
+      axis.text = element_text(size = 10, face = "bold", colour = "#F0F0F0"),
+      axis.text.x = element_text(margin = margin(t = 10), colour = "#F0F0F0"),
+      axis.text.y = element_text(margin = margin(r = 10), colour = "#F0F0F0"),
 
       # Axis titles
-      axis.title = element_text(size = 12, face = "bold", colour = "#FE9000"),  # Orange axis titles
+      axis.title = element_text(size = 12, face = "bold", colour = "#FE9000"),
       axis.title.x = element_text(size = 14, face = "bold", margin = margin(t = 10), colour = "#FE9000"),
       axis.title.y = element_text(size = 14, face = "bold", margin = margin(r = 10), colour = "#FE9000"),
 
       # Axis tick marks
-      axis.ticks = element_line(size = 0.75, colour = "#FE9000"),  # Orange axis ticks
+      axis.ticks = element_line(linewidth = 0.75, colour = "#FE9000"),
       axis.ticks.length = unit(0.3, "cm"),
 
       # Legend
-      legend.text = element_text(size = 10, colour = "#F0F0F0"),  # Light gray legend text
-      legend.title = element_text(size = 12, face = "bold", colour = "#FE9000"),  # Orange legend title
+      legend.text = element_text(size = 10, colour = "#F0F0F0"),
+      legend.title = element_text(size = 12, face = "bold", colour = "#FE9000"),
 
       # Axis line
       axis.line = element_line(
-        color = "#FE9000",  # Orange axis line
+        color = "#FE9000", # Orange axis line
         linewidth = 1,
         arrow = arrow(
           type = "closed",
@@ -128,4 +128,3 @@ theme_ggswim_dark <- function(base_size = 12, base_family = "") {
       panel.grid.minor = element_blank()
     )
 }
-

README.Rmd

@@ -48,15 +48,15 @@ library(ggplot2)
 
 # Construct arrow_data for arrow display later
 arrow_data <- patient_data |>
-    dplyr::left_join(
-      end_study_events |>
-        dplyr::select(pt_id, label),
-      by = "pt_id"
-    ) |>
-    dplyr::select(pt_id, end_time, label) |>
-    dplyr::filter(.by = pt_id, end_time == max(end_time)) |>
-    dplyr::filter(is.na(label)) |>
-    unique()
+  dplyr::left_join(
+    end_study_events |>
+      dplyr::select(pt_id, label),
+    by = "pt_id"
+  ) |>
+  dplyr::select(pt_id, end_time, label) |>
+  dplyr::filter(.by = pt_id, end_time == max(end_time)) |>
+  dplyr::filter(is.na(label)) |>
+  unique()
 
 p <- patient_data |>
   ggplot() +
@@ -100,10 +100,12 @@ This looks OK as a default, but it's not quite as nice as we'd like it to be. Le
 
 ```{r, message = FALSE}
 p <- p +
-  scale_marker_discrete(glyphs = all_events$glyph, 
-                        colours = all_events$colour, 
-                        limits = all_events$label, 
-                        name = "Study Events")
+  scale_marker_discrete(
+    glyphs = all_events$glyph,
+    colours = all_events$colour,
+    limits = all_events$label,
+    name = "Study Events"
+  )
 
 p
 ```

README.md

@@ -49,15 +49,15 @@ library(ggplot2)
 
 # Construct arrow_data for arrow display later
 arrow_data <- patient_data |>
-    dplyr::left_join(
-      end_study_events |>
-        dplyr::select(pt_id, label),
-      by = "pt_id"
-    ) |>
-    dplyr::select(pt_id, end_time, label) |>
-    dplyr::filter(.by = pt_id, end_time == max(end_time)) |>
-    dplyr::filter(is.na(label)) |>
-    unique()
+  dplyr::left_join(
+    end_study_events |>
+      dplyr::select(pt_id, label),
+    by = "pt_id"
+  ) |>
+  dplyr::select(pt_id, end_time, label) |>
+  dplyr::filter(.by = pt_id, end_time == max(end_time)) |>
+  dplyr::filter(is.na(label)) |>
+  unique()
 
 p <- patient_data |>
   ggplot() +
@@ -111,10 +111,12 @@ like to use for the markers with ggswim’s `scale_marker_discrete()`.
 
 ``` r
 p <- p +
-  scale_marker_discrete(glyphs = all_events$glyph, 
-                        colours = all_events$colour, 
-                        limits = all_events$label, 
-                        name = "Study Events")
+  scale_marker_discrete(
+    glyphs = all_events$glyph,
+    colours = all_events$colour,
+    limits = all_events$label,
+    name = "Study Events"
+  )
 
 p
 ```