Dev

.gitignore

@@ -28,3 +28,4 @@ optimizing plotly testing.X
 data-raw/catlogo.svg
 vignettes/articles/ggpedigree_config.rds
 *DESKTOP-16M0RPI's conflicted*
+/.claude

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggpedigree
 Title: Visualizing Pedigrees with 'ggplot2' and 'plotly'
-Version: 1.1.1.1
+Version: 1.1.1.9
 Date/Publication: 2026
 Authors@R: c(
     person("S. Mason", "Garrison", email= "garrissm@wfu.edu", role = c("aut", "cre", "cph"),
@@ -25,6 +25,7 @@ Imports:
     tidyr
 Suggests:
     selectr (>= 0.5-1),
+    svglite,
     kinship2,
     quadprog,
     ggrepel,

NEWS.md

@@ -1,6 +1,14 @@
 # ggpedigree (development version)
 # ==============================
 
+## New features
+* Added more flexibility to overlays, including support for shape-mode overlays with custom numeric codes and colors.
+* Added a new vignette to explain the clinical preset and its features.
+
+## Bug fixes
+* Fixed multi-overlay closure bug where all overlays were filtered on the last column in the list due to R's lazy evaluation of function arguments. Local variable assignment now forces evaluation at the correct loop iteration.
+* Fixed `preset` (e.g., `"clinical"`) not being forwarded to `getDefaultPlotConfig()` in `ggPedigree()` and `ggPedigreeInteractive()`, which meant preset-driven settings like `overlay_mode = "shape"` and `overlay_include = TRUE` were silently ignored.
+
 # ggpedigree Version: 1.1.1.1
 * Hotpatch to fix plotly vignette selectively failing by using tryCatch to catch the error and print a warning instead of failing the whole vignette build.
 * Also increased test coverage of kinship2_pedigree.

R/defaultPlotConfig.R

@@ -123,6 +123,7 @@
 #' @param status_color_affected Color for affected individuals.
 #' @param status_color_unaffected Color for unaffected individuals.
 #' @param overlay_shape  Shape used for overlaying points in the plot. Default is 4 (cross).
+#'   When overlay_mode is "shape", accepts named strings: "cross", "slash", "x".
 #' @param overlay_code_affected  Code for affected individuals in overlay. Default is 1.
 #' @param overlay_code_unaffected  Code for unaffected individuals in overlay. Default is 0.
 #' @param overlay_label_affected  Label for affected individuals in overlay. Default is "Affected".
@@ -131,6 +132,13 @@
 #' @param overlay_alpha_unaffected Alpha for unaffected individuals in overlay. Default is 0.
 #' @param overlay_color  Color for overlay points. Default is "black".
 #' @param overlay_include Whether to include overlay points in the plot. Default is FALSE.
+#' @param overlay_mode  Character string specifying the overlay rendering mode.
+#'   "alpha" (default) uses alpha transparency mapping; "shape" draws a shape overlay
+#'   on matching individuals (e.g., cross for deceased markers).
+#' @param overlay_size  Numeric. Size of the shape overlay. Default is NULL (inherits from point_size).
+#'   Only used when overlay_mode is "shape".
+#' @param overlay_stroke  Stroke width for the shape overlay. Default is 1.5.
+#'   Only used when overlay_mode is "shape".
 #' @param overlay_legend_title  Title of the overlay legend. Default is "Overlay".
 #' @param overlay_legend_show  Whether to show the overlay legend. Default is FALSE.
 #' @param focal_fill_include Whether to fill focal individuals. Default is FALSE.
@@ -186,6 +194,25 @@
 #' @param recode_missing_sex Whether to recode missing sex codes in the pedigree. Default is TRUE.
 #' @param debug Whether to enable debugging mode.
 #' @param add_phantoms Whether to add phantom parents for individuals without parents.
+#' @param affected_fill_include Whether to enable affected fill styling. Default is FALSE.
+#' @param affected_fill_code_affected Value in the affected fill column that triggers filling. Default is 1.
+#' @param affected_fill_code_unaffected Value in the affected fill column for unaffected individuals. Default is 0.
+#' @param affected_fill_label_affected Label for affected individuals in fill legend. Default is "Affected".
+#' @param affected_fill_label_unaffected Label for unaffected individuals in fill legend. Default is "Unaffected".
+#' @param affected_fill_color_affected Color used to fill symbols for affected individuals. Default is "black".
+#' @param affected_fill_color_unaffected Color used to fill symbols for unaffected individuals. Default is NA (transparent).
+#' @param affected_fill_shape_female Filled shape for affected females. Default is 21 (filled circle).
+#' @param affected_fill_shape_male Filled shape for affected males. Default is 22 (filled square).
+#' @param affected_fill_shape_unknown Filled shape for affected unknown sex. Default is 23 (filled diamond).
+#' @param outline_color_include Whether to enable column-based outline coloring. Default is FALSE.
+#' @param outline_color_code_affected Value in the outline color column that triggers colored outlines. Default is 1.
+#' @param outline_color_code_unaffected Value in the outline color column for default outlines. Default is 0.
+#' @param outline_color_label_affected Label for highlighted outline individuals. Default is "Highlighted".
+#' @param outline_color_label_unaffected Label for default outline individuals. Default is "Default".
+#' @param outline_color_affected Color used for highlighted outlines. Default is "blue".
+#' @param outline_color_unaffected Color used for default (non-highlighted) outlines. Default is "black".
+#' @param preset Optional preset name for default styling combinations.
+#'   Currently supported: "clinical" for standard clinical pedigree styling. Default is "none" (no preset).
 #' @param ... Additional arguments for future extensibility.
 #' @return A named list of default plotting and layout parameters.
 #' @export
@@ -325,6 +352,9 @@
                                  overlay_alpha_unaffected = 0,
                                  overlay_color = "black",
                                  overlay_include = FALSE,
+                                 overlay_mode = "alpha",
+                                 overlay_size = NULL,
+                                 overlay_stroke = 1.5,
                                  overlay_legend_title = "Overlay",
                                  overlay_legend_show = FALSE,
                                  # ---- Focal Fill Settings ----
@@ -408,15 +438,37 @@
                                  recode_missing_ids = TRUE,
                                  recode_missing_sex = TRUE,
                                  add_phantoms = FALSE,
+                                 # ---- Clinical Pedigree Styling ----
+                                 # -- Affected Fill --
+                                 affected_fill_include = FALSE,
+                                 affected_fill_code_affected = 1,
+                                 affected_fill_code_unaffected = 0,
+                                 affected_fill_label_affected = "Affected",
+                                 affected_fill_label_unaffected = "Unaffected",
+                                 affected_fill_color_affected = "black",
+                                 affected_fill_color_unaffected = NA,
+                                 affected_fill_shape_female = 21,
+                                 affected_fill_shape_male = 22,
+                                 affected_fill_shape_unknown = 23,
+                                 # -- Outline Color --
+                                 outline_color_include = FALSE,
+                                 outline_color_code_affected = 1,
+                                 outline_color_code_unaffected = 0,
+                                 outline_color_label_affected = "Highlighted",
+                                 outline_color_label_unaffected = "Default",
+                                 outline_color_affected = "blue",
+                                 outline_color_unaffected = "black",
+                                 # -- Preset --
+                                 preset = "none",
                                  # ---- Future Extensibility ----
                                  ...) {
   # Ensure the color palette is a character vector
   if (!is.character(color_palette_default) ||
     length(color_palette_default) < 3) {
     stop("color_palette_default must be a character vector with at least 3 colors.")
   }
   if (!is.character(segment_default_color) ||
     length(segment_default_color) != 1) {
     stop("segment_default_color must be a single character string.")
   }
 
@@ -454,7 +506,7 @@
   }
   color_theme_lower <- stringr::str_to_lower(color_theme)
 
-  if (color_theme_lower %in% c(grey_color_names, black_color_names)) {
+  if (color_theme_lower %in% c(grey_color_names, black_color_names) || identical(preset, "clinical")) {
     color_palette_default <- greyscale_palette_default
     color_palette_low <- greyscale_low
     color_palette_mid <- greyscale_mid
@@ -625,6 +677,9 @@
     overlay_color = overlay_color,
     overlay_alpha_affected = overlay_alpha_affected,
     overlay_include = overlay_include,
+    overlay_mode = overlay_mode,
+    overlay_size = overlay_size,
+    overlay_stroke = overlay_stroke,
     overlay_legend_title = overlay_legend_title,
     overlay_legend_show = overlay_legend_show,
 
@@ -691,7 +746,29 @@
     recode_missing_ids = recode_missing_ids,
     recode_missing_sex = recode_missing_sex,
     add_phantoms = add_phantoms,
-    debug = debug
+    debug = debug,
+    # ---- Clinical Pedigree Styling ----
+    # -- Affected Fill --
+    affected_fill_include = affected_fill_include,
+    affected_fill_code_affected = affected_fill_code_affected,
+    affected_fill_code_unaffected = affected_fill_code_unaffected,
+    affected_fill_label_affected = affected_fill_label_affected,
+    affected_fill_label_unaffected = affected_fill_label_unaffected,
+    affected_fill_color_affected = affected_fill_color_affected,
+    affected_fill_color_unaffected = affected_fill_color_unaffected,
+    affected_fill_shape_female = affected_fill_shape_female,
+    affected_fill_shape_male = affected_fill_shape_male,
+    affected_fill_shape_unknown = affected_fill_shape_unknown,
+    # -- Outline Color --
+    outline_color_include = outline_color_include,
+    outline_color_code_affected = outline_color_code_affected,
+    outline_color_code_unaffected = outline_color_code_unaffected,
+    outline_color_label_affected = outline_color_label_affected,
+    outline_color_label_unaffected = outline_color_label_unaffected,
+    outline_color_affected = outline_color_affected,
+    outline_color_unaffected = outline_color_unaffected,
+    # -- Preset --
+    preset = preset
   )
   lc_function_name <- stringr::str_to_lower(function_name)
   if (lc_function_name %in% c("ggrelatednessmatrix")) {
@@ -713,7 +790,7 @@
     core_list$return_widget <- FALSE
     core_list$return_interactive <- FALSE
   } else if (lc_function_name %in%
     c("ggphenotypebydegree", "phenotypebydegree")) {
     core_list$point_size <- 1
     core_list$plot_title <- "Phenotypic Correlation vs Genetic Relatedness"
     core_list$return_static <- FALSE
@@ -781,6 +858,18 @@
     core_list$segment_self_angle <- -75
     core_list$segment_self_curvature <- -0.15
   }
-
+  # Apply clinical preset if specified
+  if (identical(preset, "clinical")) {
+    # Clinical defaults: shape by sex, unfilled by default, blue outline for included
+    core_list$sex_color_include <- FALSE
+    core_list$sex_shape_include <- TRUE
+    core_list$outline_include <- TRUE
+    core_list$outline_color <- core_list$outline_color_unaffected
+    # Configure overlay for shape mode (e.g., cross for deceased markers)
+    core_list$overlay_include <- TRUE
+    core_list$overlay_mode <- "shape"
+    core_list$overlay_shape <- 4 # Cross shape
+    core_list$overlay_color <- core_list$color_palette_high
+  }
   core_list
 }

R/ggPedigreeInteractive.R

@@ -60,7 +60,9 @@
                                   return_widget = TRUE,
                                   hints = NULL,
                                   code_male = NULL,
-                                  sexVar = "sex") {
+                                  sexVar = "sex",
+                                  affected_fill_column = NULL,
+                                  outline_color_column = NULL) {
   if (!requireNamespace("plotly", quietly = TRUE)) {
     stop("The 'plotly' package is required for interactive plots.")
   }
@@ -98,6 +100,7 @@
   default_config <- getDefaultPlotConfig(
     function_name = "ggPedigreeInteractive",
     personID = personID,
+    preset = if (is.null(config$preset)) "none" else config$preset,
     color_theme = ifelse(is.null(config$color_theme), "color", config$color_theme)
   )
 
@@ -130,7 +133,9 @@
     debug = config$debug,
     focal_fill_column = focal_fill_column,
     function_name = "ggPedigreeInteractive",
-    sexVar = sexVar
+    sexVar = sexVar,
+    affected_fill_column = affected_fill_column,
+    outline_color_column = outline_color_column
   )
 
   ## 2. Identify data columns for tooltips ----------------------------------
@@ -304,7 +309,7 @@
 #' "spousehint", "parent_fam", "nid", "x_order",
 #' "y_order", "y_fam", "zygosity", "extra", and "x_fam".
 #' @return The optimized ggplot object with rounded coordinates and reduced data frame.
 #' @keywords internal
 
 
 optimizeStaticPedigree <- function(p, config = list(), variable_drop = c(

R/ggpedigree.R

@@ -19,6 +19,15 @@
 #' @param hints Data frame with hints for layout adjustments. Default: NULL.
 #' @param interactive Logical. If TRUE, generates an interactive plot using `plotly`. Default: FALSE.
 #' @param overlay_column Character string specifying the column name for overlay alpha values.
+#'   For a single overlay, this is the simplest interface. For multiple overlays, use
+#'   the \code{overlays} parameter instead.
+#' @param overlays A list of overlay specifications for adding multiple independent overlay
+#'   layers. Each element should be a list with at minimum a \code{column} entry, plus optional
+#'   entries: \code{code_affected}, \code{shape}, \code{color}, \code{size}, \code{stroke},
+#'   \code{mode}. Unspecified entries inherit from the \code{overlay_*} config defaults.
+#'   When \code{overlays} is provided, \code{overlay_column} is ignored.
+#'   Example: \code{overlays = list(list(column = "DECES", shape = "cross"),
+#'   list(column = "PROBAND", shape = 8, color = "red"))}
 #' @param tooltip_columns Character vector of column names to show when hovering.
 #'        Defaults to c("personID", "sex").  Additional columns present in `ped`
 #'        can be supplied – they will be added to the Plotly tooltip text.
@@ -29,6 +38,12 @@
 #' @param code_male Integer or string. Value identifying males in the sex column. (typically 0 or 1) Default: 1
 #' @param sexVar Character string specifying the column name for sex. Defaults to "sex".
 #' @param focal_fill_column Character string specifying the column name for focal fill color.
+#' @param affected_fill_column Character string specifying the column name for conditional
+#'   affected fill. When provided, individuals matching the `affected_fill_code_affected` config
+#'   will have their symbols filled. Default is NULL.
+#' @param outline_color_column Character string specifying the column name for outline
+#'   color control. When provided, individuals matching `outline_color_code_affected` config
+#'   will have colored outlines (e.g., blue for included). Default is NULL.
 #' @param config A list of configuration options for customizing the plot.
 #'        See getDefaultPlotConfig for details of each option. The list can include:
 #'  \describe{
@@ -79,13 +94,16 @@
                        focal_fill_column = NULL,
                        tooltip_columns = NULL,
                        overlay_column = NULL,
+                       overlays = NULL,
                        return_widget = FALSE,
                        config = list(),
                        debug = FALSE,
                        hints = NULL,
                        interactive = FALSE,
                        code_male = NULL,
-                       sexVar = "sex") {
+                       sexVar = "sex",
+                       affected_fill_column = NULL,
+                       outline_color_column = NULL) {
   if (!inherits(ped, "data.frame")) {
     if (rlang::inherits_any(ped, c("ped", "pedigree", "kinship2.pedigree"))) {
       # Convert ped object to data.frame
@@ -103,7 +121,7 @@
   }
 
   if (interactive == TRUE &&
     requireNamespace("plotly", quietly = TRUE)) {
     # Call the interactive function with the provided arguments
 
     ggPedigreeInteractive(
@@ -125,11 +143,13 @@
       return_widget = return_widget,
       tooltip_columns = tooltip_columns,
       code_male = code_male,
-      sexVar = sexVar
+      sexVar = sexVar,
+      affected_fill_column = affected_fill_column,
+      outline_color_column = outline_color_column
     )
   } else {
     if (interactive == TRUE &&
       !requireNamespace("plotly", quietly = TRUE)) {
       message("The 'plotly' package is required for interactive plots.")
     }
 
@@ -137,6 +157,7 @@
     default_config <- getDefaultPlotConfig(
       function_name = "ggpedigree",
       personID = personID,
+      preset = if (is.null(config$preset)) "none" else config$preset,
       color_theme = ifelse(is.null(config$color_theme), "color", config$color_theme)
     )
 
@@ -166,13 +187,16 @@
       matID = matID,
       patID = patID,
       overlay_column = overlay_column,
+      overlays = overlays,
       twinID = twinID,
       status_column = status_column,
       focal_fill_column = focal_fill_column,
       config = config,
       debug = debug,
       hints = hints,
-      sexVar = sexVar
+      sexVar = sexVar,
+      affected_fill_column = affected_fill_column,
+      outline_color_column = outline_color_column
     )
   }
 }