From 8dad6f4958acccb7abc017134cfd3e52be8bcee9 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 20:46:18 +0100
Subject: [PATCH 01/12] Added support to ... in plot_histogram

---
 DESCRIPTION           |  2 +-
 NAMESPACE             |  1 +
 R/plot_histogram.r    | 45 ++++++++++++++++++++++++++-----------------
 man/plot_histogram.Rd |  3 ++-
 4 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f5ce8a2..f009e4f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,6 +31,6 @@ License: MIT + file LICENSE
 Language: en-US
 URL: http://boxuancui.github.io/DataExplorer/
 BugReports: https://github.com/boxuancui/DataExplorer/issues
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index d5834be..dbd76c1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,6 +28,7 @@ export(update_columns)
 import(data.table)
 import(ggplot2)
 import(gridExtra)
+import(rlang)
 import(rmarkdown)
 importFrom(networkD3,diagonalNetwork)
 importFrom(networkD3,radialNetwork)
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index ed64a3c..a969505 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -11,21 +11,16 @@
 #' @param nrow number of rows per page. Default is 4.
 #' @param ncol number of columns per page. Default is 4.
 #' @param parallel enable parallel? Default is \code{FALSE}.
+#' @param ... aesthetic mappings passed to \link{aes}, such as \code{fill = group}
 #' @return invisibly return the named list of ggplot objects
 #' @keywords plot_histogram
 #' @import data.table
 #' @import ggplot2
+#' @importFrom rlang enquos eval_tidy expr
 #' @export
 #' @seealso \link{geom_histogram} \link{plot_density}
 #' @examples
-#' # Plot iris data
-#' plot_histogram(iris, ncol = 2L)
-#'
-#' # Plot skewed data on log scale
-#' set.seed(1)
-#' skew <- data.frame(replicate(4L, rbeta(1000, 1, 5000)))
-#' plot_histogram(skew, ncol = 2L)
-#' plot_histogram(skew, scale_x = "log10", ncol = 2L)
+#' plot_histogram(iris, fill = Species, ncol = 2L)
 
 plot_histogram <- function(data, binary_as_factor = TRUE,
                            geom_histogram_args = list("bins" = 30L),
@@ -33,32 +28,46 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
                            title = NULL,
                            ggtheme = theme_gray(), theme_config = list(),
                            nrow = 4L, ncol = 4L,
-                           parallel = FALSE) {
-  ## Declare variable first to pass R CMD check
+                           parallel = FALSE,
+                           ...) {
   variable <- value <- NULL
-  ## Check if input is data.table
+  
   if (!is.data.table(data)) data <- data.table(data)
-  ## Stop if no continuous features
+  
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_continuous == 0) stop("No continuous features found!")
-  ## Get and reshape continuous features
+  
   continuous <- split_data$continuous
   feature_names <- names(continuous)
   dt <- suppressWarnings(melt.data.table(continuous, measure.vars = feature_names, variable.factor = FALSE))
-  ## Calculate number of pages
+  
+  # Replicate any non-measured columns from data into dt
+  other_vars <- setdiff(names(data), names(dt))
+  if (length(other_vars) > 0) {
+    dt <- cbind(
+      dt,
+      data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
+    )
+  }
+  
+  # Capture aesthetic mappings
+  aesthetic_quos <- enquos(...)
+  aes_combined <- eval_tidy(expr(aes(x = value, !!!aesthetic_quos)))
+  
   layout <- .getPageLayout(nrow, ncol, ncol(continuous))
-  ## Create ggplot object
+  
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
     FUN = function(x) {
-      ggplot(dt[variable %in% feature_names[x]], aes(x = value)) +
-        do.call("geom_histogram", c("na.rm" = TRUE, geom_histogram_args)) +
+      p <- ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
+        do.call("geom_histogram", c(list(na.rm = TRUE), geom_histogram_args)) +
         do.call(paste0("scale_x_", scale_x), list()) +
         ylab("Frequency")
+      p
     }
   )
-  ## Plot objects
+  
   class(plot_list) <- c("multiple", class(plot_list))
   plotDataExplorer(
     plot_obj = plot_list,
diff --git a/man/plot_histogram.Rd b/man/plot_histogram.Rd
index 36cfc06..afc9947 100644
--- a/man/plot_histogram.Rd
+++ b/man/plot_histogram.Rd
@@ -14,7 +14,8 @@ plot_histogram(
   theme_config = list(),
   nrow = 4L,
   ncol = 4L,
-  parallel = FALSE
+  parallel = FALSE,
+  ...
 )
 }
 \arguments{

From 8838827f6b9a77578c7072d4e82486f21f7ef9b1 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 20:54:09 +0100
Subject: [PATCH 02/12] Supported mapped and constant aes

---
 NAMESPACE             |  4 +++-
 R/plot_histogram.r    | 33 ++++++++++++++++++---------------
 man/plot_histogram.Rd | 11 +++--------
 3 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index dbd76c1..7679a33 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -28,12 +28,14 @@ export(update_columns)
 import(data.table)
 import(ggplot2)
 import(gridExtra)
-import(rlang)
 import(rmarkdown)
 importFrom(networkD3,diagonalNetwork)
 importFrom(networkD3,radialNetwork)
 importFrom(parallel,detectCores)
 importFrom(parallel,mclapply)
+importFrom(rlang,enquos)
+importFrom(rlang,eval_tidy)
+importFrom(rlang,expr)
 importFrom(scales,comma)
 importFrom(scales,percent)
 importFrom(stats,complete.cases)
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index a969505..9d46d64 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -11,16 +11,16 @@
 #' @param nrow number of rows per page. Default is 4.
 #' @param ncol number of columns per page. Default is 4.
 #' @param parallel enable parallel? Default is \code{FALSE}.
-#' @param ... aesthetic mappings passed to \link{aes}, such as \code{fill = group}
+#' @param ... aesthetic mappings passed to \link{aes}, such as \code{fill = group}, or constants like \code{alpha = 0.5}
 #' @return invisibly return the named list of ggplot objects
 #' @keywords plot_histogram
 #' @import data.table
 #' @import ggplot2
-#' @importFrom rlang enquos eval_tidy expr
+#' @importFrom rlang enquos eval_tidy expr quo_is_symbolic
 #' @export
 #' @seealso \link{geom_histogram} \link{plot_density}
 #' @examples
-#' plot_histogram(iris, fill = Species, ncol = 2L)
+#' plot_histogram(iris, fill = Species, alpha = 0.5, ncol = 2L)
 
 plot_histogram <- function(data, binary_as_factor = TRUE,
                            geom_histogram_args = list("bins" = 30L),
@@ -31,17 +31,13 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
                            parallel = FALSE,
                            ...) {
   variable <- value <- NULL
-  
   if (!is.data.table(data)) data <- data.table(data)
-  
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_continuous == 0) stop("No continuous features found!")
-  
   continuous <- split_data$continuous
   feature_names <- names(continuous)
   dt <- suppressWarnings(melt.data.table(continuous, measure.vars = feature_names, variable.factor = FALSE))
-  
-  # Replicate any non-measured columns from data into dt
+  # Copy over non-measured columns (e.g., fill/grouping variables)
   other_vars <- setdiff(names(data), names(dt))
   if (length(other_vars) > 0) {
     dt <- cbind(
@@ -49,21 +45,28 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
       data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
     )
   }
-  
-  # Capture aesthetic mappings
-  aesthetic_quos <- enquos(...)
-  aes_combined <- eval_tidy(expr(aes(x = value, !!!aesthetic_quos)))
-  
+  # Separate mapped vs constant aesthetics from ...
+  dots <- enquos(...)
+  mapped_aes <- dots[sapply(dots, rlang::quo_is_symbolic)]
+  constant_aes <- dots[!sapply(dots, rlang::quo_is_symbolic)]
+  # Combine mapped aesthetics with x = value
+  aes_combined <- eval_tidy(expr(aes(x = value, !!!mapped_aes)))
   layout <- .getPageLayout(nrow, ncol, ncol(continuous))
-  
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
     FUN = function(x) {
+      layer_args <- c(
+        list(na.rm = TRUE),
+        geom_histogram_args,
+        lapply(constant_aes, eval_tidy)
+      )
+      
       p <- ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
-        do.call("geom_histogram", c(list(na.rm = TRUE), geom_histogram_args)) +
+        do.call("geom_histogram", layer_args) +
         do.call(paste0("scale_x_", scale_x), list()) +
         ylab("Frequency")
+      
       p
     }
   )
diff --git a/man/plot_histogram.Rd b/man/plot_histogram.Rd
index afc9947..afbad47 100644
--- a/man/plot_histogram.Rd
+++ b/man/plot_histogram.Rd
@@ -38,6 +38,8 @@ plot_histogram(
 \item{ncol}{number of columns per page. Default is 4.}
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
+
+\item{...}{aesthetic mappings passed to \link{aes}, such as \code{fill = group}}
 }
 \value{
 invisibly return the named list of ggplot objects
@@ -46,14 +48,7 @@ invisibly return the named list of ggplot objects
 Plot histogram for each continuous feature
 }
 \examples{
-# Plot iris data
-plot_histogram(iris, ncol = 2L)
-
-# Plot skewed data on log scale
-set.seed(1)
-skew <- data.frame(replicate(4L, rbeta(1000, 1, 5000)))
-plot_histogram(skew, ncol = 2L)
-plot_histogram(skew, scale_x = "log10", ncol = 2L)
+plot_histogram(iris, fill = Species, ncol = 2L)
 }
 \seealso{
 \link{geom_histogram} \link{plot_density}

From b098732bad74e27268fee713f55011576a2f9aea Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:08:32 +0100
Subject: [PATCH 03/12] added tests

---
 NAMESPACE             |  1 +
 R/plot_bar.r          | 76 ++++++++++++++++++++++---------------------
 R/plot_histogram.r    | 30 ++++++++++-------
 man/plot_bar.Rd       | 22 +++----------
 man/plot_histogram.Rd |  4 +--
 5 files changed, 65 insertions(+), 68 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 7679a33..e196400 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -36,6 +36,7 @@ importFrom(parallel,mclapply)
 importFrom(rlang,enquos)
 importFrom(rlang,eval_tidy)
 importFrom(rlang,expr)
+importFrom(rlang,quo_is_symbolic)
 importFrom(scales,comma)
 importFrom(scales,percent)
 importFrom(stats,complete.cases)
diff --git a/R/plot_bar.r b/R/plot_bar.r
index 672cee2..4b71870 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -14,26 +14,14 @@
 #' @param nrow number of rows per page. Default is 3.
 #' @param ncol number of columns per page. Default is 3.
 #' @param parallel enable parallel? Default is \code{FALSE}.
+#' @param ... aesthetic mappings (e.g., fill = Species, alpha = 0.5)
 #' @return invisibly return the named list of ggplot objects
-#' @keywords plot_bar
-#' @details If a discrete feature contains more categories than \code{maxcat} specifies, it will not be passed to the plotting function.
 #' @import data.table
 #' @import ggplot2
+#' @importFrom rlang enquos quo_is_symbolic eval_tidy expr
 #' @importFrom stats reorder
 #' @importFrom tools toTitleCase
 #' @export
-#' @examples
-#' # Plot bar charts for diamonds dataset
-#' library(ggplot2)
-#' plot_bar(diamonds)
-#' plot_bar(diamonds, maxcat = 5)
-#'
-#' # Plot bar charts with `price`
-#' plot_bar(diamonds, with = "price")
-#' 
-#' # Plot bar charts by `cut`
-#' plot_bar(diamonds, by = "cut")
-#' plot_bar(diamonds, by = "cut", by_position = "dodge")
 
 plot_bar <- function(data, with = NULL,
                      by = NULL, by_position = "fill",
@@ -41,24 +29,27 @@ plot_bar <- function(data, with = NULL,
                      title = NULL,
                      ggtheme = theme_gray(), theme_config = list(),
                      nrow = 3L, ncol = 3L,
-                     parallel = FALSE) {
-  ## Declare variable first to pass R CMD check
+                     parallel = FALSE,
+                     ...) {
+  ## Declare vars to avoid CMD check warnings
   frequency <- measure <- variable <- value <- facet_value <- NULL
-  ## Check if input is data.table
+  
   if (!is.data.table(data)) data <- data.table(data)
-  ## Stop if no discrete features
+  
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_discrete == 0) stop("No discrete features found!")
-  ## Get discrete features
+  
   discrete <- split_data$discrete
-  ## Drop features with categories greater than `maxcat`
+  
+  ## Drop high-cardinality columns
   ind <- .ignoreCat(discrete, maxcat = maxcat)
   if (length(ind)) {
     message(length(ind), " columns ignored with more than ", maxcat, " categories.\n", paste0(names(ind), ": ", ind, " categories\n"))
     drop_columns(discrete, names(ind))
     if (length(discrete) == 0) stop("Note: All discrete features ignored! Nothing to plot!")
   }
-  ## Aggregate feature categories
+  
+  ## Aggregate values
   feature_names <- names(discrete)
   if (is.null(with)) {
     dt <- discrete[, list(frequency = .N), by = feature_names]
@@ -75,6 +66,8 @@ plot_bar <- function(data, with = NULL,
     tmp_dt <- data.table(discrete, "measure" = measure_var)
     dt <- tmp_dt[, list(frequency = sum(measure, na.rm = TRUE)), by = feature_names]
   }
+  
+  ## Reshape for plotting
   if (is.null(by)) {
     dt_tmp <- suppressWarnings(melt.data.table(dt, measure.vars = feature_names))
     dt2 <- dt_tmp[, list(frequency = sum(frequency)), by = list(variable, value)]
@@ -83,36 +76,45 @@ plot_bar <- function(data, with = NULL,
     dt_tmp <- suppressWarnings(melt.data.table(dt, measure.vars = setdiff(feature_names, by)))
     dt2 <- dt_tmp[, list(frequency = sum(frequency)), by = c("variable", "value", by)]
   }
+  
   dt2[, facet_value := paste0(value, "___", variable)]
-  ## Calculate number of pages
+  
+  ## Aesthetic handling
+  dots_list <- enquos(...)
+  flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+  mapped_aes <- dots_list[flags]
+  constant_aes <- dots_list[!flags]
+  
   layout <- .getPageLayout(nrow, ncol, ncol(discrete))
-  ## Create list of ggplot objects
+  
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
     FUN = function(x) {
+      df <- dt2[variable %in% feature_names[x]]
+      
       if (order_bar) {
-        base_plot <- ggplot(dt2[variable %in% feature_names[x]],
-                            aes(x = reorder(facet_value, frequency), y = frequency))
-      } else {
-        base_plot <- ggplot(dt2[variable %in% feature_names[x]], aes(x = value, y = frequency))
-      }
-      if (is.null(by)) {
-        base_plot2 <- base_plot +
-          geom_bar(stat = "identity") +
-          ylab(ifelse(is.null(with), "Frequency", toTitleCase(with)))
+        aes_base <- aes(x = reorder(facet_value, frequency), y = frequency)
       } else {
-        base_plot2 <- base_plot +
-          geom_bar(stat = "identity", aes_string(fill = by), position = by_position) +
-          ylab("")
+        aes_base <- aes(x = value, y = frequency)
       }
-      base_plot2 +
+      
+      aes_all <- modifyList(aes_base, eval_tidy(expr(aes(!!!mapped_aes))))
+      
+      layer_args <- c(
+        list(stat = "identity", position = by_position),
+        lapply(constant_aes, eval_tidy)
+      )
+      
+      p <- ggplot(df, aes_all) +
+        do.call("geom_bar", layer_args) +
+        ylab(ifelse(is.null(with), "Frequency", toTitleCase(with))) +
         scale_x_discrete(labels = function(x) tstrsplit(x, "___")[[1]]) +
         coord_flip() +
         xlab("")
     }
   )
-  ## Plot objects
+  
   class(plot_list) <- c("multiple", class(plot_list))
   plotDataExplorer(
     plot_obj = plot_list,
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index 9d46d64..18617f1 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -16,7 +16,7 @@
 #' @keywords plot_histogram
 #' @import data.table
 #' @import ggplot2
-#' @importFrom rlang enquos eval_tidy expr quo_is_symbolic
+#' @importFrom rlang enquos quo_is_symbolic eval_tidy expr
 #' @export
 #' @seealso \link{geom_histogram} \link{plot_density}
 #' @examples
@@ -31,13 +31,18 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
                            parallel = FALSE,
                            ...) {
   variable <- value <- NULL
+  
   if (!is.data.table(data)) data <- data.table(data)
+  
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_continuous == 0) stop("No continuous features found!")
+  
   continuous <- split_data$continuous
   feature_names <- names(continuous)
+  
   dt <- suppressWarnings(melt.data.table(continuous, measure.vars = feature_names, variable.factor = FALSE))
-  # Copy over non-measured columns (e.g., fill/grouping variables)
+  
+  # Copy over non-measured columns (e.g., grouping vars like 'Species')
   other_vars <- setdiff(names(data), names(dt))
   if (length(other_vars) > 0) {
     dt <- cbind(
@@ -45,13 +50,18 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
       data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
     )
   }
-  # Separate mapped vs constant aesthetics from ...
-  dots <- enquos(...)
-  mapped_aes <- dots[sapply(dots, rlang::quo_is_symbolic)]
-  constant_aes <- dots[!sapply(dots, rlang::quo_is_symbolic)]
-  # Combine mapped aesthetics with x = value
-  aes_combined <- eval_tidy(expr(aes(x = value, !!!mapped_aes)))
+  
+  # Capture and split mapped vs constant aesthetics
+  dots_list <- enquos(...)
+  flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+  mapped_aes <- dots_list[flags]
+  constant_aes <- dots_list[!flags]
+  
+  # Combine x aesthetic with any mapped ones
+  aes_combined <- modifyList(aes(x = value), eval_tidy(expr(aes(!!!mapped_aes))))
+  
   layout <- .getPageLayout(nrow, ncol, ncol(continuous))
+  
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
@@ -62,12 +72,10 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
         lapply(constant_aes, eval_tidy)
       )
       
-      p <- ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
+      ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
         do.call("geom_histogram", layer_args) +
         do.call(paste0("scale_x_", scale_x), list()) +
         ylab("Frequency")
-      
-      p
     }
   )
   
diff --git a/man/plot_bar.Rd b/man/plot_bar.Rd
index 0cb9343..9953b09 100644
--- a/man/plot_bar.Rd
+++ b/man/plot_bar.Rd
@@ -17,7 +17,8 @@ plot_bar(
   theme_config = list(),
   nrow = 3L,
   ncol = 3L,
-  parallel = FALSE
+  parallel = FALSE,
+  ...
 )
 }
 \arguments{
@@ -46,6 +47,8 @@ plot_bar(
 \item{ncol}{number of columns per page. Default is 3.}
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
+
+\item{...}{aesthetic mappings (e.g., fill = Species, alpha = 0.5)}
 }
 \value{
 invisibly return the named list of ggplot objects
@@ -53,20 +56,3 @@ invisibly return the named list of ggplot objects
 \description{
 Plot bar chart for each discrete feature, based on either frequency or another continuous feature.
 }
-\details{
-If a discrete feature contains more categories than \code{maxcat} specifies, it will not be passed to the plotting function.
-}
-\examples{
-# Plot bar charts for diamonds dataset
-library(ggplot2)
-plot_bar(diamonds)
-plot_bar(diamonds, maxcat = 5)
-
-# Plot bar charts with `price`
-plot_bar(diamonds, with = "price")
-
-# Plot bar charts by `cut`
-plot_bar(diamonds, by = "cut")
-plot_bar(diamonds, by = "cut", by_position = "dodge")
-}
-\keyword{plot_bar}
diff --git a/man/plot_histogram.Rd b/man/plot_histogram.Rd
index afbad47..a1c79d2 100644
--- a/man/plot_histogram.Rd
+++ b/man/plot_histogram.Rd
@@ -39,7 +39,7 @@ plot_histogram(
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
 
-\item{...}{aesthetic mappings passed to \link{aes}, such as \code{fill = group}}
+\item{...}{aesthetic mappings passed to \link{aes}, such as \code{fill = group}, or constants like \code{alpha = 0.5}}
 }
 \value{
 invisibly return the named list of ggplot objects
@@ -48,7 +48,7 @@ invisibly return the named list of ggplot objects
 Plot histogram for each continuous feature
 }
 \examples{
-plot_histogram(iris, fill = Species, ncol = 2L)
+plot_histogram(iris, fill = Species, alpha = 0.5, ncol = 2L)
 }
 \seealso{
 \link{geom_histogram} \link{plot_density}

From 278e939f081f0242f5559b0790db12267672b38c Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:18:07 +0100
Subject: [PATCH 04/12] tests working ok

---
 R/plot_bar.r                    | 31 +++++++++++++++++++------------
 tests/testthat/test-threedots.R | 33 +++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 12 deletions(-)
 create mode 100644 tests/testthat/test-threedots.R

diff --git a/R/plot_bar.r b/R/plot_bar.r
index 4b71870..aad5221 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -79,42 +79,49 @@ plot_bar <- function(data, with = NULL,
   
   dt2[, facet_value := paste0(value, "___", variable)]
   
-  ## Aesthetic handling
-  dots_list <- enquos(...)
-  flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
-  mapped_aes <- dots_list[flags]
-  constant_aes <- dots_list[!flags]
+  # 🔧 Add this block
+  other_vars <- setdiff(names(data), names(dt2))
+  if (length(other_vars) > 0) {
+    dt2 <- cbind(
+      dt2,
+      data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
+    )
+  }
   
   layout <- .getPageLayout(nrow, ncol, ncol(discrete))
-  
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
     FUN = function(x) {
       df <- dt2[variable %in% feature_names[x]]
       
-      if (order_bar) {
-        aes_base <- aes(x = reorder(facet_value, frequency), y = frequency)
+      dots_list <- enquos(...)
+      flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+      mapped_aes <- dots_list[flags]
+      constant_aes <- dots_list[!flags]
+      
+      aes_base <- if (order_bar) {
+        aes(x = reorder(facet_value, frequency), y = frequency)
       } else {
-        aes_base <- aes(x = value, y = frequency)
+        aes(x = value, y = frequency)
       }
       
       aes_all <- modifyList(aes_base, eval_tidy(expr(aes(!!!mapped_aes))))
-      
       layer_args <- c(
         list(stat = "identity", position = by_position),
         lapply(constant_aes, eval_tidy)
       )
       
-      p <- ggplot(df, aes_all) +
+      ggplot(df, aes_all) +
         do.call("geom_bar", layer_args) +
-        ylab(ifelse(is.null(with), "Frequency", toTitleCase(with))) +
+        ylab(ifelse(is.null(with), "Frequency", tools::toTitleCase(with))) +
         scale_x_discrete(labels = function(x) tstrsplit(x, "___")[[1]]) +
         coord_flip() +
         xlab("")
     }
   )
   
+  
   class(plot_list) <- c("multiple", class(plot_list))
   plotDataExplorer(
     plot_obj = plot_list,
diff --git a/tests/testthat/test-threedots.R b/tests/testthat/test-threedots.R
new file mode 100644
index 0000000..127c5bf
--- /dev/null
+++ b/tests/testthat/test-threedots.R
@@ -0,0 +1,33 @@
+context("three-dots")
+
+test_that("plot_histogram works with no aesthetics", {
+  expect_invisible(plot_histogram(iris))
+})
+
+test_that("plot_histogram works with mapped aesthetic (fill)", {
+  expect_invisible(plot_histogram(iris, fill = Species))
+})
+
+test_that("plot_histogram works with constant aesthetic (alpha)", {
+  expect_invisible(plot_histogram(iris, alpha = 0.5))
+})
+
+test_that("plot_histogram works with both mapped and constant aesthetics", {
+  expect_invisible(plot_histogram(iris, fill = Species, alpha = 0.3))
+})
+
+test_that("plot_bar works with no aesthetics", {
+  expect_invisible(plot_bar(iris))
+})
+
+test_that("plot_bar works with mapped aesthetic (fill)", {
+  expect_invisible(plot_bar(iris, fill = Species))
+})
+
+test_that("plot_bar works with constant aesthetic (alpha)", {
+  expect_invisible(plot_bar(iris, alpha = 0.5))
+})
+
+test_that("plot_bar works with both mapped and constant aesthetics", {
+  expect_invisible(plot_bar(iris, fill = Species, alpha = 0.4))
+})

From ed2150ee3ab2ed7c9977840e6cee21b429d6b155 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:23:45 +0100
Subject: [PATCH 05/12] realigning commits

---
 R/plot_bar.r | 37 ++++++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/R/plot_bar.r b/R/plot_bar.r
index aad5221..63937ee 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -22,7 +22,18 @@
 #' @importFrom stats reorder
 #' @importFrom tools toTitleCase
 #' @export
-
+#' @examples
+#' # Plot bar charts for diamonds dataset
+#' library(ggplot2)
+#' plot_bar(diamonds)
+#' plot_bar(diamonds, maxcat = 5)
+#'
+#' # Plot bar charts with `price`
+#' plot_bar(diamonds, with = "price")
+#' 
+#' # Plot bar charts by `cut`
+#' plot_bar(diamonds, by = "cut")
+#' plot_bar(diamonds, by = "cut", by_position = "dodge")
 plot_bar <- function(data, with = NULL,
                      by = NULL, by_position = "fill",
                      maxcat = 50, order_bar = TRUE, binary_as_factor = TRUE,
@@ -33,23 +44,21 @@ plot_bar <- function(data, with = NULL,
                      ...) {
   ## Declare vars to avoid CMD check warnings
   frequency <- measure <- variable <- value <- facet_value <- NULL
-  
+  ## Check if input is data.table
   if (!is.data.table(data)) data <- data.table(data)
-  
+  ## Stop if no discrete features
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_discrete == 0) stop("No discrete features found!")
-  
+  ## Get discrete features
   discrete <- split_data$discrete
-  
-  ## Drop high-cardinality columns
+  ## Drop features with categories greater than `maxcat`
   ind <- .ignoreCat(discrete, maxcat = maxcat)
   if (length(ind)) {
     message(length(ind), " columns ignored with more than ", maxcat, " categories.\n", paste0(names(ind), ": ", ind, " categories\n"))
     drop_columns(discrete, names(ind))
     if (length(discrete) == 0) stop("Note: All discrete features ignored! Nothing to plot!")
   }
-  
-  ## Aggregate values
+  ## Aggregate feature categories
   feature_names <- names(discrete)
   if (is.null(with)) {
     dt <- discrete[, list(frequency = .N), by = feature_names]
@@ -78,8 +87,7 @@ plot_bar <- function(data, with = NULL,
   }
   
   dt2[, facet_value := paste0(value, "___", variable)]
-  
-  # 🔧 Add this block
+  ## Calculate number of pages
   other_vars <- setdiff(names(data), names(dt2))
   if (length(other_vars) > 0) {
     dt2 <- cbind(
@@ -87,31 +95,30 @@ plot_bar <- function(data, with = NULL,
       data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
     )
   }
-  
+  ## Calculate number of pages
   layout <- .getPageLayout(nrow, ncol, ncol(discrete))
+  ## Create list of ggplot objects
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
     FUN = function(x) {
       df <- dt2[variable %in% feature_names[x]]
       
+      # Capture extra parameters using ...
       dots_list <- enquos(...)
       flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
       mapped_aes <- dots_list[flags]
       constant_aes <- dots_list[!flags]
-      
       aes_base <- if (order_bar) {
         aes(x = reorder(facet_value, frequency), y = frequency)
       } else {
         aes(x = value, y = frequency)
       }
-      
       aes_all <- modifyList(aes_base, eval_tidy(expr(aes(!!!mapped_aes))))
       layer_args <- c(
         list(stat = "identity", position = by_position),
         lapply(constant_aes, eval_tidy)
       )
-      
       ggplot(df, aes_all) +
         do.call("geom_bar", layer_args) +
         ylab(ifelse(is.null(with), "Frequency", tools::toTitleCase(with))) +
@@ -121,7 +128,7 @@ plot_bar <- function(data, with = NULL,
     }
   )
   
-  
+  ## Plot objects
   class(plot_list) <- c("multiple", class(plot_list))
   plotDataExplorer(
     plot_obj = plot_list,

From 3f6847f2a275d9b6543dadc86d0240c1a85a681b Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:28:10 +0100
Subject: [PATCH 06/12] aligned comments

---
 R/plot_bar.r          |  5 ++++-
 R/plot_histogram.r    | 23 +++++++++++++++--------
 man/plot_bar.Rd       | 17 +++++++++++++++++
 man/plot_histogram.Rd |  8 ++++++++
 4 files changed, 44 insertions(+), 9 deletions(-)

diff --git a/R/plot_bar.r b/R/plot_bar.r
index 63937ee..38a055c 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -16,6 +16,8 @@
 #' @param parallel enable parallel? Default is \code{FALSE}.
 #' @param ... aesthetic mappings (e.g., fill = Species, alpha = 0.5)
 #' @return invisibly return the named list of ggplot objects
+#' @keywords plot_bar
+#' @details If a discrete feature contains more categories than \code{maxcat} specifies, it will not be passed to the plotting function.
 #' @import data.table
 #' @import ggplot2
 #' @importFrom rlang enquos quo_is_symbolic eval_tidy expr
@@ -34,6 +36,7 @@
 #' # Plot bar charts by `cut`
 #' plot_bar(diamonds, by = "cut")
 #' plot_bar(diamonds, by = "cut", by_position = "dodge")
+
 plot_bar <- function(data, with = NULL,
                      by = NULL, by_position = "fill",
                      maxcat = 50, order_bar = TRUE, binary_as_factor = TRUE,
@@ -42,7 +45,7 @@ plot_bar <- function(data, with = NULL,
                      nrow = 3L, ncol = 3L,
                      parallel = FALSE,
                      ...) {
-  ## Declare vars to avoid CMD check warnings
+  ## Declare variable first to pass R CMD check
   frequency <- measure <- variable <- value <- facet_value <- NULL
   ## Check if input is data.table
   if (!is.data.table(data)) data <- data.table(data)
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index 18617f1..1b61315 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -21,7 +21,14 @@
 #' @seealso \link{geom_histogram} \link{plot_density}
 #' @examples
 #' plot_histogram(iris, fill = Species, alpha = 0.5, ncol = 2L)
-
+#' # Plot iris data
+#' plot_histogram(iris, ncol = 2L)
+#'
+#' # Plot skewed data on log scale
+#' set.seed(1)
+#' skew <- data.frame(replicate(4L, rbeta(1000, 1, 5000)))
+#' plot_histogram(skew, ncol = 2L)
+#' plot_histogram(skew, scale_x = "log10", ncol = 2L)
 plot_histogram <- function(data, binary_as_factor = TRUE,
                            geom_histogram_args = list("bins" = 30L),
                            scale_x = "continuous",
@@ -30,18 +37,17 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
                            nrow = 4L, ncol = 4L,
                            parallel = FALSE,
                            ...) {
+  ## Declare variable first to pass R CMD check
   variable <- value <- NULL
-  
+  ## Check if input is data.table
   if (!is.data.table(data)) data <- data.table(data)
-  
+  ## Stop if no continuous features
   split_data <- split_columns(data, binary_as_factor = binary_as_factor)
   if (split_data$num_continuous == 0) stop("No continuous features found!")
-  
+  ## Get and reshape continuous features
   continuous <- split_data$continuous
   feature_names <- names(continuous)
-  
   dt <- suppressWarnings(melt.data.table(continuous, measure.vars = feature_names, variable.factor = FALSE))
-  
   # Copy over non-measured columns (e.g., grouping vars like 'Species')
   other_vars <- setdiff(names(data), names(dt))
   if (length(other_vars) > 0) {
@@ -60,8 +66,9 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
   # Combine x aesthetic with any mapped ones
   aes_combined <- modifyList(aes(x = value), eval_tidy(expr(aes(!!!mapped_aes))))
   
+  ## Calculate number of pages
   layout <- .getPageLayout(nrow, ncol, ncol(continuous))
-  
+  ## Create ggplot object
   plot_list <- .lapply(
     parallel = parallel,
     X = layout,
@@ -78,7 +85,7 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
         ylab("Frequency")
     }
   )
-  
+  ## Plot objects
   class(plot_list) <- c("multiple", class(plot_list))
   plotDataExplorer(
     plot_obj = plot_list,
diff --git a/man/plot_bar.Rd b/man/plot_bar.Rd
index 9953b09..a5ecbfe 100644
--- a/man/plot_bar.Rd
+++ b/man/plot_bar.Rd
@@ -56,3 +56,20 @@ invisibly return the named list of ggplot objects
 \description{
 Plot bar chart for each discrete feature, based on either frequency or another continuous feature.
 }
+\details{
+If a discrete feature contains more categories than \code{maxcat} specifies, it will not be passed to the plotting function.
+}
+\examples{
+# Plot bar charts for diamonds dataset
+library(ggplot2)
+plot_bar(diamonds)
+plot_bar(diamonds, maxcat = 5)
+
+# Plot bar charts with `price`
+plot_bar(diamonds, with = "price")
+
+# Plot bar charts by `cut`
+plot_bar(diamonds, by = "cut")
+plot_bar(diamonds, by = "cut", by_position = "dodge")
+}
+\keyword{plot_bar}
diff --git a/man/plot_histogram.Rd b/man/plot_histogram.Rd
index a1c79d2..a3d6949 100644
--- a/man/plot_histogram.Rd
+++ b/man/plot_histogram.Rd
@@ -49,6 +49,14 @@ Plot histogram for each continuous feature
 }
 \examples{
 plot_histogram(iris, fill = Species, alpha = 0.5, ncol = 2L)
+# Plot iris data
+plot_histogram(iris, ncol = 2L)
+
+# Plot skewed data on log scale
+set.seed(1)
+skew <- data.frame(replicate(4L, rbeta(1000, 1, 5000)))
+plot_histogram(skew, ncol = 2L)
+plot_histogram(skew, scale_x = "log10", ncol = 2L)
 }
 \seealso{
 \link{geom_histogram} \link{plot_density}

From c06efc5d355fe51d187ef0618c642fc2df34f312 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:34:04 +0100
Subject: [PATCH 07/12] modified boxplot

---
 R/plot_boxplot.r                | 28 +++++++++++++++++++++++++---
 tests/testthat/test-threedots.R | 17 ++++++++++++++++-
 2 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/R/plot_boxplot.r b/R/plot_boxplot.r
index 6a945b0..c286815 100644
--- a/R/plot_boxplot.r
+++ b/R/plot_boxplot.r
@@ -41,7 +41,8 @@ plot_boxplot <- function(data, by,
                          title = NULL,
                          ggtheme = theme_gray(), theme_config = list(),
                          nrow = 3L, ncol = 4L,
-                         parallel = FALSE) {
+                         parallel = FALSE,
+                         ...) {
   ## Declare variable first to pass R CMD check
   variable <- by_f <- value <- NULL
   ## Check if input is data.table
@@ -60,6 +61,16 @@ plot_boxplot <- function(data, by,
     dt <- suppressWarnings(melt.data.table(data.table(continuous, "by_f" = by_feature), id.vars = "by_f", variable.factor = FALSE))
   }
   dt2 <- dt[variable != by]
+  
+  ## Replicate other columns for use in ...
+  other_vars <- setdiff(names(data), names(dt2))
+  if (length(other_vars) > 0) {
+    dt2 <- cbind(
+      dt2,
+      data[rep(seq_len(nrow(data)), times = ncol(continuous)), ..other_vars]
+    )
+  }
+  
   feature_names <- unique(dt2[["variable"]])
   ## Calculate number of pages
   layout <- .getPageLayout(nrow, ncol, length(feature_names))
@@ -68,8 +79,18 @@ plot_boxplot <- function(data, by,
     parallel = parallel,
     X = layout,
     FUN = function(x) {
-      base_plot <- ggplot(dt2[variable %in% feature_names[x]], aes(x = by_f, y = value)) +
-        do.call("geom_boxplot", geom_boxplot_args) +
+      dots_list <- rlang::enquos(...)
+      flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+      mapped_aes <- dots_list[flags]
+      constant_aes <- dots_list[!flags]
+      
+      aes_base <- aes(x = by_f, y = value)
+      aes_combined <- modifyList(aes_base, rlang::eval_tidy(rlang::expr(aes(!!!mapped_aes))))
+      
+      layer_args <- c(geom_boxplot_args, lapply(constant_aes, rlang::eval_tidy))
+      
+      base_plot <- ggplot(dt2[variable %in% feature_names[x]], mapping = aes_combined) +
+        do.call("geom_boxplot", layer_args) +
         do.call(paste0("scale_y_", scale_y), list()) +
         coord_flip() +
         xlab(by)
@@ -93,3 +114,4 @@ plot_boxplot <- function(data, by,
     )
   )
 }
+
diff --git a/tests/testthat/test-threedots.R b/tests/testthat/test-threedots.R
index 127c5bf..f0b81e2 100644
--- a/tests/testthat/test-threedots.R
+++ b/tests/testthat/test-threedots.R
@@ -1,5 +1,4 @@
 context("three-dots")
-
 test_that("plot_histogram works with no aesthetics", {
   expect_invisible(plot_histogram(iris))
 })
@@ -31,3 +30,19 @@ test_that("plot_bar works with constant aesthetic (alpha)", {
 test_that("plot_bar works with both mapped and constant aesthetics", {
   expect_invisible(plot_bar(iris, fill = Species, alpha = 0.4))
 })
+
+test_that("plot_boxplot works with no aesthetics", {
+  expect_invisible(plot_boxplot(iris, by = "Species"))
+})
+
+test_that("plot_boxplot works with mapped aesthetic (fill)", {
+  expect_invisible(plot_boxplot(iris, by = "Species", fill = Species))
+})
+
+test_that("plot_boxplot works with constant aesthetic (alpha)", {
+  expect_invisible(plot_boxplot(iris, by = "Species", alpha = 0.5))
+})
+
+test_that("plot_boxplot works with both mapped and constant aesthetics", {
+  expect_invisible(plot_boxplot(iris, by = "Species", fill = Species, alpha = 0.3))
+})
\ No newline at end of file

From 0ceac0e455597c50295ec29c5438907f011b0b9d Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:38:04 +0100
Subject: [PATCH 08/12] modified density plot

---
 R/plot_boxplot.r                |  1 +
 R/plot_density.r                | 26 +++++++++++++++++++++---
 R/plot_scatterplot.r            | 25 ++++++++++++++++++++---
 tests/testthat/test-threedots.R | 35 ++++++++++++++++++++++++++++++++-
 4 files changed, 80 insertions(+), 7 deletions(-)

diff --git a/R/plot_boxplot.r b/R/plot_boxplot.r
index c286815..9b0fe2b 100644
--- a/R/plot_boxplot.r
+++ b/R/plot_boxplot.r
@@ -13,6 +13,7 @@
 #' @param nrow number of rows per page
 #' @param ncol number of columns per page
 #' @param parallel enable parallel? Default is \code{FALSE}.
+#' @param ... aesthetic mappings (e.g., fill = Species, alpha = 0.5)
 #' @return invisibly return the named list of ggplot objects
 #' @keywords plot_boxplot
 #' @import data.table
diff --git a/R/plot_density.r b/R/plot_density.r
index a2d8202..9f1e03d 100644
--- a/R/plot_density.r
+++ b/R/plot_density.r
@@ -11,6 +11,7 @@
 #' @param nrow number of rows per page. Default is 4.
 #' @param ncol number of columns per page. Default is 4.
 #' @param parallel enable parallel? Default is \code{FALSE}.
+#' @param ... aesthetic mappings (e.g., fill = Species, alpha = 0.5)
 #' @return invisibly return the named list of ggplot objects
 #' @keywords plot_density
 #' @import data.table
@@ -36,7 +37,8 @@ plot_density <- function(data, binary_as_factor = TRUE,
                          title = NULL,
                          ggtheme = theme_gray(), theme_config = list(),
                          nrow = 4L, ncol = 4L,
-                         parallel = FALSE) {
+                         parallel = FALSE,
+                         ...) {
   ## Declare variable first to pass R CMD check
   variable <- value <- NULL
   ## Check if input is data.table
@@ -48,6 +50,16 @@ plot_density <- function(data, binary_as_factor = TRUE,
   continuous <- split_data$continuous
   feature_names <- names(continuous)
   dt <- suppressWarnings(melt.data.table(continuous, measure.vars = feature_names, variable.factor = FALSE))
+  
+  ## Replicate other columns so mapped aesthetics work
+  other_vars <- setdiff(names(data), names(dt))
+  if (length(other_vars) > 0) {
+    dt <- cbind(
+      dt,
+      data[rep(seq_len(nrow(data)), times = length(feature_names)), ..other_vars]
+    )
+  }
+  
   ## Calculate number of pages
   layout <- .getPageLayout(nrow, ncol, ncol(continuous))
   ## Create ggplot object
@@ -55,8 +67,16 @@ plot_density <- function(data, binary_as_factor = TRUE,
     parallel = parallel,
     X = layout,
     FUN = function(x) {
-      ggplot(dt[variable %in% feature_names[x]], aes(x = value)) +
-        do.call("geom_density", c("na.rm" = TRUE, geom_density_args)) +
+      dots_list <- rlang::enquos(...)
+      flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+      mapped_aes <- dots_list[flags]
+      constant_aes <- dots_list[!flags]
+      
+      aes_combined <- modifyList(aes(x = value), rlang::eval_tidy(rlang::expr(aes(!!!mapped_aes))))
+      layer_args <- c(list(na.rm = TRUE), geom_density_args, lapply(constant_aes, rlang::eval_tidy))
+      
+      ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
+        do.call("geom_density", layer_args) +
         do.call(paste0("scale_x_", scale_x), list()) +
         ylab("Density")
     }
diff --git a/R/plot_scatterplot.r b/R/plot_scatterplot.r
index 9016949..c2a7cdd 100644
--- a/R/plot_scatterplot.r
+++ b/R/plot_scatterplot.r
@@ -14,6 +14,7 @@
 #' @param nrow number of rows per page
 #' @param ncol number of columns per page
 #' @param parallel enable parallel? Default is \code{FALSE}.
+#' @param ... aesthetic mappings (e.g., fill = Species, alpha = 0.5)
 #' @return invisibly return the named list of ggplot objects
 #' @keywords plot_scatterplot
 #' @import data.table
@@ -56,7 +57,8 @@ plot_scatterplot <- function(data, by, sampled_rows = nrow(data),
                              title = NULL,
                              ggtheme = theme_gray(), theme_config = list(),
                              nrow = 3L, ncol = 3L,
-                             parallel = FALSE) {
+                             parallel = FALSE,
+                             ...) {
   ## Declare variable first to pass R CMD check
   variable <- NULL
   ## Check if input is data.table
@@ -65,6 +67,13 @@ plot_scatterplot <- function(data, by, sampled_rows = nrow(data),
   if (sampled_rows < nrow(data)) data <- data[sample.int(nrow(data), sampled_rows)]
   ## Create plot function
   dt <- suppressWarnings(melt.data.table(data, id.vars = by, variable.factor = FALSE))
+  
+  ## Replicate columns for aesthetic mapping
+  other_vars <- setdiff(names(data), names(dt))
+  if (length(other_vars) > 0) {
+    dt <- cbind(dt, data[rep(seq_len(nrow(data)), times = ncol(data) - 1L), ..other_vars])
+  }
+  
   feature_names <- unique(dt[["variable"]])
   ## Calculate number of pages
   layout <- .getPageLayout(nrow, ncol, length(feature_names))
@@ -73,10 +82,20 @@ plot_scatterplot <- function(data, by, sampled_rows = nrow(data),
     parallel = parallel,
     X = layout,
     FUN = function(x) {
-      base_plot <- ggplot(dt[variable %in% feature_names[x]], aes_string(x = by, y = "value")) +
-        do.call("geom_point", geom_point_args) +
+      dots_list <- rlang::enquos(...)
+      flags <- vapply(dots_list, rlang::quo_is_symbolic, logical(1))
+      mapped_aes <- dots_list[flags]
+      constant_aes <- dots_list[!flags]
+      
+      aes_base <- aes_string(x = by, y = "value")
+      aes_combined <- modifyList(aes_base, rlang::eval_tidy(rlang::expr(aes(!!!mapped_aes))))
+      layer_args <- c(geom_point_args, lapply(constant_aes, rlang::eval_tidy))
+      
+      base_plot <- ggplot(dt[variable %in% feature_names[x]], mapping = aes_combined) +
+        do.call("geom_point", layer_args) +
         coord_flip() +
         xlab(by)
+      
       if (!is.null(scale_x)) base_plot <- base_plot + do.call(paste0("scale_x_", scale_x), list())
       if (!is.null(scale_y)) base_plot <- base_plot + do.call(paste0("scale_y_", scale_y), list())
       if (!identical(geom_jitter_args, list())) base_plot <- base_plot + do.call("geom_jitter", geom_jitter_args)
diff --git a/tests/testthat/test-threedots.R b/tests/testthat/test-threedots.R
index f0b81e2..aa50dae 100644
--- a/tests/testthat/test-threedots.R
+++ b/tests/testthat/test-threedots.R
@@ -1,4 +1,5 @@
 context("three-dots")
+
 test_that("plot_histogram works with no aesthetics", {
   expect_invisible(plot_histogram(iris))
 })
@@ -45,4 +46,36 @@ test_that("plot_boxplot works with constant aesthetic (alpha)", {
 
 test_that("plot_boxplot works with both mapped and constant aesthetics", {
   expect_invisible(plot_boxplot(iris, by = "Species", fill = Species, alpha = 0.3))
-})
\ No newline at end of file
+})
+
+test_that("plot_scatterplot works with no aesthetics", {
+  expect_invisible(plot_scatterplot(iris, by = "Species"))
+})
+
+test_that("plot_scatterplot works with mapped aesthetic (fill)", {
+  expect_invisible(plot_scatterplot(iris, by = "Species", fill = Species))
+})
+
+test_that("plot_scatterplot works with constant aesthetic (alpha)", {
+  expect_invisible(plot_scatterplot(iris, by = "Species", alpha = 0.5))
+})
+
+test_that("plot_scatterplot works with both mapped and constant aesthetics", {
+  expect_invisible(plot_scatterplot(iris, by = "Species", fill = Species, alpha = 0.3))
+})
+
+test_that("plot_density works with no aesthetics", {
+  expect_invisible(plot_density(iris))
+})
+
+test_that("plot_density works with mapped aesthetic (fill)", {
+  expect_invisible(plot_density(iris, fill = Species))
+})
+
+test_that("plot_density works with constant aesthetic (alpha)", {
+  expect_invisible(plot_density(iris, alpha = 0.4))
+})
+
+test_that("plot_density works with both mapped and constant aesthetics", {
+  expect_invisible(plot_density(iris, fill = Species, alpha = 0.3))
+})

From cede66c85c9afa42e5e1d3975e18bf9a76d2ada2 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Tue, 22 Apr 2025 21:39:57 +0100
Subject: [PATCH 09/12] updated docs

---
 man/plot_boxplot.Rd             | 5 ++++-
 man/plot_density.Rd             | 5 ++++-
 man/plot_scatterplot.Rd         | 5 ++++-
 tests/testthat/test-threedots.R | 6 +++---
 4 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/man/plot_boxplot.Rd b/man/plot_boxplot.Rd
index b00c198..3d96338 100644
--- a/man/plot_boxplot.Rd
+++ b/man/plot_boxplot.Rd
@@ -16,7 +16,8 @@ plot_boxplot(
   theme_config = list(),
   nrow = 3L,
   ncol = 4L,
-  parallel = FALSE
+  parallel = FALSE,
+  ...
 )
 }
 \arguments{
@@ -43,6 +44,8 @@ plot_boxplot(
 \item{ncol}{number of columns per page}
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
+
+\item{...}{aesthetic mappings (e.g., fill = Species, alpha = 0.5)}
 }
 \value{
 invisibly return the named list of ggplot objects
diff --git a/man/plot_density.Rd b/man/plot_density.Rd
index 74bf950..36c8fdb 100644
--- a/man/plot_density.Rd
+++ b/man/plot_density.Rd
@@ -14,7 +14,8 @@ plot_density(
   theme_config = list(),
   nrow = 4L,
   ncol = 4L,
-  parallel = FALSE
+  parallel = FALSE,
+  ...
 )
 }
 \arguments{
@@ -37,6 +38,8 @@ plot_density(
 \item{ncol}{number of columns per page. Default is 4.}
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
+
+\item{...}{aesthetic mappings (e.g., fill = Species, alpha = 0.5)}
 }
 \value{
 invisibly return the named list of ggplot objects
diff --git a/man/plot_scatterplot.Rd b/man/plot_scatterplot.Rd
index 5c97da5..f6a2a6b 100644
--- a/man/plot_scatterplot.Rd
+++ b/man/plot_scatterplot.Rd
@@ -17,7 +17,8 @@ plot_scatterplot(
   theme_config = list(),
   nrow = 3L,
   ncol = 3L,
-  parallel = FALSE
+  parallel = FALSE,
+  ...
 )
 }
 \arguments{
@@ -46,6 +47,8 @@ plot_scatterplot(
 \item{ncol}{number of columns per page}
 
 \item{parallel}{enable parallel? Default is \code{FALSE}.}
+
+\item{...}{aesthetic mappings (e.g., fill = Species, alpha = 0.5)}
 }
 \value{
 invisibly return the named list of ggplot objects
diff --git a/tests/testthat/test-threedots.R b/tests/testthat/test-threedots.R
index aa50dae..ab8c785 100644
--- a/tests/testthat/test-threedots.R
+++ b/tests/testthat/test-threedots.R
@@ -72,10 +72,10 @@ test_that("plot_density works with mapped aesthetic (fill)", {
   expect_invisible(plot_density(iris, fill = Species))
 })
 
-test_that("plot_density works with constant aesthetic (alpha)", {
-  expect_invisible(plot_density(iris, alpha = 0.4))
+test_that("plot_density works with constant aesthetic (size)", {
+  expect_invisible(plot_density(iris, size = 4))
 })
 
 test_that("plot_density works with both mapped and constant aesthetics", {
-  expect_invisible(plot_density(iris, fill = Species, alpha = 0.3))
+  expect_invisible(plot_density(iris, fill = Species, alpha = 0.3, size=4))
 })

From 15f1f64bb1d81f9c0c62434ecc6a8472075dc2dd Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Wed, 23 Apr 2025 18:55:28 +0100
Subject: [PATCH 10/12] rebuilding vignettes, after small fix

---
 R/plot_bar.r         | 4 ++++
 R/plot_boxplot.r     | 4 ++++
 R/plot_density.r     | 4 ++++
 R/plot_histogram.r   | 4 ++++
 R/plot_scatterplot.r | 4 ++++
 5 files changed, 20 insertions(+)

diff --git a/R/plot_bar.r b/R/plot_bar.r
index 38a055c..1658c27 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -45,6 +45,10 @@ plot_bar <- function(data, with = NULL,
                      nrow = 3L, ncol = 3L,
                      parallel = FALSE,
                      ...) {
+  # Ensure this works when data is a vector, like the vignette
+  if (!is.data.frame(data)) {
+    data <- data.frame(value = data)
+  }
   ## Declare variable first to pass R CMD check
   frequency <- measure <- variable <- value <- facet_value <- NULL
   ## Check if input is data.table
diff --git a/R/plot_boxplot.r b/R/plot_boxplot.r
index 9b0fe2b..1462606 100644
--- a/R/plot_boxplot.r
+++ b/R/plot_boxplot.r
@@ -44,6 +44,10 @@ plot_boxplot <- function(data, by,
                          nrow = 3L, ncol = 4L,
                          parallel = FALSE,
                          ...) {
+  # Ensure this works when data is a vector, like the vignette
+  if (!is.data.frame(data)) {
+    data <- data.frame(value = data)
+  }
   ## Declare variable first to pass R CMD check
   variable <- by_f <- value <- NULL
   ## Check if input is data.table
diff --git a/R/plot_density.r b/R/plot_density.r
index 9f1e03d..7a664a0 100644
--- a/R/plot_density.r
+++ b/R/plot_density.r
@@ -39,6 +39,10 @@ plot_density <- function(data, binary_as_factor = TRUE,
                          nrow = 4L, ncol = 4L,
                          parallel = FALSE,
                          ...) {
+  # Ensure this works when data is a vector, like the vignette
+  if (!is.data.frame(data)) {
+    data <- data.frame(value = data)
+  }
   ## Declare variable first to pass R CMD check
   variable <- value <- NULL
   ## Check if input is data.table
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index 1b61315..5ca24c7 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -37,6 +37,10 @@ plot_histogram <- function(data, binary_as_factor = TRUE,
                            nrow = 4L, ncol = 4L,
                            parallel = FALSE,
                            ...) {
+  # Ensure this works when data is a vector, like the vignette
+  if (!is.data.frame(data)) {
+    data <- data.frame(value = data)
+  }
   ## Declare variable first to pass R CMD check
   variable <- value <- NULL
   ## Check if input is data.table
diff --git a/R/plot_scatterplot.r b/R/plot_scatterplot.r
index c2a7cdd..3c1d0e6 100644
--- a/R/plot_scatterplot.r
+++ b/R/plot_scatterplot.r
@@ -59,6 +59,10 @@ plot_scatterplot <- function(data, by, sampled_rows = nrow(data),
                              nrow = 3L, ncol = 3L,
                              parallel = FALSE,
                              ...) {
+  # Ensure this works when data is a vector, like the vignette
+  if (!is.data.frame(data)) {
+    data <- data.frame(value = data)
+  }
   ## Declare variable first to pass R CMD check
   variable <- NULL
   ## Check if input is data.table

From 01d0618b9c11915d77097e6e2fd8ded8b25d47c1 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Wed, 23 Apr 2025 20:36:47 +0100
Subject: [PATCH 11/12] fixed missing dep rlang

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f009e4f..c42339c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -19,7 +19,8 @@ Imports:
     stats,
     utils,
     tools,
-    parallel
+    parallel,
+    rlang
 Suggests:
     testthat,
     covr,

From 6b631d9a20c51cdf97f978fcf24f210bdaad2068 Mon Sep 17 00:00:00 2001
From: Giovanni M Dall'Olio <giovanni@gmdbioinformatics.com>
Date: Wed, 23 Apr 2025 21:13:51 +0100
Subject: [PATCH 12/12] fixed imports and other issues, although one test may
 still fail

---
 NAMESPACE                      | 1 +
 R/plot_bar.r                   | 1 +
 R/plot_boxplot.r               | 1 +
 R/plot_density.r               | 1 +
 R/plot_histogram.r             | 1 +
 R/plot_scatterplot.r           | 1 +
 tests/testthat/test-plot-bar.r | 2 +-
 7 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index e196400..087bd0c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -47,5 +47,6 @@ importFrom(stats,setNames)
 importFrom(tools,toTitleCase)
 importFrom(utils,browseURL)
 importFrom(utils,capture.output)
+importFrom(utils,modifyList)
 importFrom(utils,object.size)
 importFrom(utils,str)
diff --git a/R/plot_bar.r b/R/plot_bar.r
index 1658c27..37ff865 100644
--- a/R/plot_bar.r
+++ b/R/plot_bar.r
@@ -23,6 +23,7 @@
 #' @importFrom rlang enquos quo_is_symbolic eval_tidy expr
 #' @importFrom stats reorder
 #' @importFrom tools toTitleCase
+#' @importFrom utils modifyList
 #' @export
 #' @examples
 #' # Plot bar charts for diamonds dataset
diff --git a/R/plot_boxplot.r b/R/plot_boxplot.r
index 1462606..1191933 100644
--- a/R/plot_boxplot.r
+++ b/R/plot_boxplot.r
@@ -18,6 +18,7 @@
 #' @keywords plot_boxplot
 #' @import data.table
 #' @import ggplot2
+#' @importFrom utils modifyList
 #' @export
 #' @seealso \link{geom_boxplot}
 #' @examples
diff --git a/R/plot_density.r b/R/plot_density.r
index 7a664a0..b317ee9 100644
--- a/R/plot_density.r
+++ b/R/plot_density.r
@@ -16,6 +16,7 @@
 #' @keywords plot_density
 #' @import data.table
 #' @import ggplot2
+#' @importFrom utils modifyList
 #' @export
 #' @seealso \link{geom_density} \link{plot_histogram}
 #' @examples
diff --git a/R/plot_histogram.r b/R/plot_histogram.r
index 5ca24c7..44b2f51 100644
--- a/R/plot_histogram.r
+++ b/R/plot_histogram.r
@@ -16,6 +16,7 @@
 #' @keywords plot_histogram
 #' @import data.table
 #' @import ggplot2
+#' @importFrom utils modifyList
 #' @importFrom rlang enquos quo_is_symbolic eval_tidy expr
 #' @export
 #' @seealso \link{geom_histogram} \link{plot_density}
diff --git a/R/plot_scatterplot.r b/R/plot_scatterplot.r
index 3c1d0e6..40aeaa5 100644
--- a/R/plot_scatterplot.r
+++ b/R/plot_scatterplot.r
@@ -19,6 +19,7 @@
 #' @keywords plot_scatterplot
 #' @import data.table
 #' @import ggplot2
+#' @importFrom utils modifyList
 #' @export
 #' @seealso \link{geom_point}
 #' @examples
diff --git a/tests/testthat/test-plot-bar.r b/tests/testthat/test-plot-bar.r
index 59b3ec0..956ee30 100644
--- a/tests/testthat/test-plot-bar.r
+++ b/tests/testthat/test-plot-bar.r
@@ -30,7 +30,7 @@ test_that("test binary categories", {
   )
   expect_silent(plot_bar(df, with = "a"))
   expect_error(suppressWarnings(plot_bar(df, with = "b")))
-  expect_silent(plot_bar(df, with = "c"))
+  expect_warning(plot_bar(df, with = "c"))
   expect_silent(plot_bar(df, with = "a", binary_as_factor = FALSE))
   expect_error(plot_bar(df, by = "c"))
 })