From 81085811d6e8cc8b82c66626667fd356329fa872 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:00:05 +0000
Subject: [PATCH 01/10] RStudio addin to define new panels.

---
 DESCRIPTION               |   5 +-
 NAMESPACE                 |   3 ++
 R/addin.R                 |  39 ++++++++++++++
 inst/rstudio/addins.dcf   |   4 ++
 inst/scripts/new_panel.R  |  44 ++++++++++++++++
 inst/templates/NewPanel.R | 106 ++++++++++++++++++++++++++++++++++++++
 man/new_panel_file.Rd     |  27 ++++++++++
 7 files changed, 226 insertions(+), 2 deletions(-)
 create mode 100644 R/addin.R
 create mode 100644 inst/rstudio/addins.dcf
 create mode 100644 inst/scripts/new_panel.R
 create mode 100644 inst/templates/NewPanel.R
 create mode 100644 man/new_panel_file.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index fe5a357..6dfd794 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -39,9 +39,10 @@ Suggests:
     knitr,
     rmarkdown,
     BiocStyle,
-    htmltools
+    htmltools,
+    rstudioapi
 URL: https://github.com/csoneson/iSEEu
 BugReports: https://github.com/csoneson/iSEEu/issues
-RoxygenNote: 7.0.1
+RoxygenNote: 7.0.2
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
index 97afc44..2806c8d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,10 @@
 
 export(modeEmpty)
 export(modeGating)
+export(new_panel_file)
 importFrom(S4Vectors,DataFrame)
 importFrom(iSEE,featAssayPlotDefaults)
 importFrom(iSEE,iSEE)
+importFrom(methods,extends)
+importFrom(methods,getClasses)
 importFrom(shiny,runApp)
diff --git a/R/addin.R b/R/addin.R
new file mode 100644
index 0000000..e1bf17a
--- /dev/null
+++ b/R/addin.R
@@ -0,0 +1,39 @@
+new_panel_addin = function() {
+  sys.source(system.file(package = 'iSEE', 'scripts', 'new_panel.R'))
+}
+
+#' @importFrom methods extends getClasses
+collect_parents <- function() {
+	x <- getClasses("package:iSEE")
+	is_panel <- function(Class) {
+		extends(Class, "Panel")
+	}
+	keep <- vapply(x, is_panel, FUN.VALUE = logical(1))
+	x[keep]
+}
+
+#' Create a new panel file
+#'
+#' Opens a template R script in the editor, to define a new iSEE panel class .
+#'
+#' @param encoded Name of the new panel class.
+#' @param decoded Extended name of the new panel class (for display).
+#' @param parent Name of the parent panel class
+#'
+#' @export
+#'
+#' @author Kevin Rue-Albrecht
+#'
+#' @seealso \linkS4class{Panel}
+#'
+#' @examples
+#' new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+new_panel_file <- function(encoded, decoded, parent="Panel") {
+  template_file <- system.file(package = "iSEE", "templates", "NewPanel.R")
+  template_content <- scan(template_file, "character", sep = "\n", quiet = TRUE)
+  template_content <- paste0(template_content, collapse = "\n")
+  template_content <- gsub("__ENCODED__", encoded, template_content, fixed = TRUE)
+  template_content <- gsub("__DECODED__", decoded, template_content, fixed = TRUE)
+  template_content <- gsub("__PARENT__", parent, template_content, fixed = TRUE)
+  rstudioapi::documentNew(template_content, type = "r")
+}
diff --git a/inst/rstudio/addins.dcf b/inst/rstudio/addins.dcf
new file mode 100644
index 0000000..61b68d1
--- /dev/null
+++ b/inst/rstudio/addins.dcf
@@ -0,0 +1,4 @@
+Name: New Panel
+Description: Create a new panel class with iSEE::new_panel().
+Binding: new_panel_addin
+Interactive: true
diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
new file mode 100644
index 0000000..f465aab
--- /dev/null
+++ b/inst/scripts/new_panel.R
@@ -0,0 +1,44 @@
+local({
+  txt_input = function(..., width = '100%') shiny::textInput(..., width = width)
+  sel_input = function(...) shiny::selectizeInput(
+    ..., width = '98%', multiple = FALSE, options = list(create = TRUE)
+  )
+  parent_choices = sort(iSEE:::collect_parents())
+  shiny::runGadget(
+    miniUI::miniPage(miniUI::miniContentPanel(
+      txt_input('encoded', 'Class encoded name', placeholder = 'MyNewPlot'),
+      txt_input('decoded', 'Class decoded name', placeholder = 'My New Plot'),
+      shiny::fillRow(
+        sel_input('parentclass', 'Parent class', parent_choices, selected="Panel"),
+        height = '70px'
+      ),
+      miniUI::gadgetTitleBar(NULL)
+    )),
+    server = function(input, output, session) {
+
+      shiny::observeEvent(input$done, {
+        encoded <- input$encoded
+        decoded <- input$decoded
+        parentclass <- input$parentclass
+
+        if (grepl('^\\s*$', encoded)) return(
+          warning('The decoded class name is empty!', call. = FALSE)
+        )
+        if (grepl('^\\s*$', decoded)) return(
+          warning('The encoded class name is empty!', call. = FALSE)
+        )
+        if (grepl('^\\s*$', parentclass)) return(
+          warning('The parent class name is empty!', call. = FALSE)
+        )
+
+        iSEE:::new_panel_file(encoded, decoded, parentclass)
+        shiny::stopApp()
+      })
+
+      shiny::observeEvent(input$cancel, {
+        shiny::stopApp()
+      })
+    },
+    stopOnCancel = FALSE, viewer = shiny::dialogViewer('New Post', height = 500)
+  )
+})
diff --git a/inst/templates/NewPanel.R b/inst/templates/NewPanel.R
new file mode 100644
index 0000000..f380725
--- /dev/null
+++ b/inst/templates/NewPanel.R
@@ -0,0 +1,106 @@
+setClass("__ENCODED__", contains="__PARENT__")
+
+#' Panel name
+#'
+#' Panel description
+#'
+#' @section Constructor:
+#' \code{__ENCODED__()} creates an instance of a __ENCODED__ class.
+#'
+#' @author Author name
+#'
+#' @examples
+#' #################
+#' # For end-users #
+#' #################
+#'
+#' x <- __ENCODED__()
+#'
+#' ##################
+#' # For developers #
+#' ##################
+#'
+#'
+#' library(scater)
+#' sce <- mockSCE()
+#' sce <- logNormCounts(sce)
+#'
+#' # Spits out a NULL and a warning if no reducedDims are available.
+#' sce0 <- .cacheCommonInfo(x, sce)
+#' .refineParameters(x, sce0)
+#'
+#' # Replaces the default with something sensible.
+#' sce <- runPCA(sce)
+#' sce0 <- .cacheCommonInfo(x, sce)
+#' .refineParameters(x, sce0)
+#'
+#' @docType methods
+#' @aliases __ENCODED__ __ENCODED__-class
+#' .defineParamInterface,__ENCODED__-method
+#' .createParamObservers,__ENCODED__-method
+#' @name __ENCODED__
+NULL
+
+#' @export
+__ENCODED__ <- function() {
+    new("__ENCODED__")
+}
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod("initialize", "__ENCODED__", function(.Object, ...) {
+    .Object <- callNextMethod(.Object, ...)
+    .Object
+})
+
+#' @export
+#' @importClassesFrom SingleCellExperiment SingleCellExperiment
+#' @importFrom methods callNextMethod
+setMethod(".cacheCommonInfo", "__ENCODED__", function(x, se) {
+    callNextMethod()
+})
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod(".refineParameters", "__ENCODED__", function(x, se) {
+    x <- callNextMethod()
+    x
+})
+
+#' @importFrom S4Vectors setValidity2
+setValidity2("__ENCODED__", function(object) {
+    msg <- character(0)
+
+    if (length(msg)>0) {
+        return(msg)
+    }
+    TRUE
+})
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod(".defineParamInterface", "__ENCODED__", function(x, se, active_panels) {
+    callNextMethod()
+})
+
+#' @export
+#' @importFrom methods callNextMethod
+setMethod(".createParamObservers", "__ENCODED__", function(x, se, input, session, pObjects, rObjects) {
+    callNextMethod()
+})
+
+#' @export
+setMethod(".get__ENCODED__", "__ENCODED__", function(x) "__ENCODED__")
+
+#' @export
+setMethod(".getFullName", "__ENCODED__", function(x) "__DECODED__")
+
+#' @export
+setMethod(".getCommandsDataXY", "__ENCODED__", function(x, param_choices) {
+    callNextMethod()
+})
+
+#' @export
+setMethod(".getCommandsPlot", "__ENCODED__", function(x, param_choices, plot_data, plot_type, labs, is_subsetted, is_downsampled) {
+    callNextMethod()
+})
diff --git a/man/new_panel_file.Rd b/man/new_panel_file.Rd
new file mode 100644
index 0000000..290fe9a
--- /dev/null
+++ b/man/new_panel_file.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/addin.R
+\name{new_panel_file}
+\alias{new_panel_file}
+\title{Create a new panel file}
+\usage{
+new_panel_file(encoded, decoded, parent = "Panel")
+}
+\arguments{
+\item{encoded}{Name of the new panel class.}
+
+\item{decoded}{Extended name of the new panel class (for display).}
+
+\item{parent}{Name of the parent panel class}
+}
+\description{
+Opens a template R script in the editor, to define a new iSEE panel class .
+}
+\examples{
+new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+}
+\seealso{
+\linkS4class{Panel}
+}
+\author{
+Kevin Rue-Albrecht
+}

From 567c223e033bd866b8bfab043fcf2f00e8baf4d6 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:02:37 +0000
Subject: [PATCH 02/10] allow future panels defined in iSEEu as parent classes

---
 R/addin.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/addin.R b/R/addin.R
index e1bf17a..579e096 100644
--- a/R/addin.R
+++ b/R/addin.R
@@ -4,7 +4,7 @@ new_panel_addin = function() {
 
 #' @importFrom methods extends getClasses
 collect_parents <- function() {
-	x <- getClasses("package:iSEE")
+	x <- unique(c(getClasses("package:iSEE"), getClasses("package:iSEEu")))
 	is_panel <- function(Class) {
 		extends(Class, "Panel")
 	}

From 67fc4b3bd0aa68e187fbaaf56c12310e62a85bc7 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:06:33 +0000
Subject: [PATCH 03/10] Cleaned up specific leftovers in the template.

---
 inst/templates/NewPanel.R | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/inst/templates/NewPanel.R b/inst/templates/NewPanel.R
index f380725..e8b51c2 100644
--- a/inst/templates/NewPanel.R
+++ b/inst/templates/NewPanel.R
@@ -25,10 +25,6 @@ setClass("__ENCODED__", contains="__PARENT__")
 #' sce <- mockSCE()
 #' sce <- logNormCounts(sce)
 #'
-#' # Spits out a NULL and a warning if no reducedDims are available.
-#' sce0 <- .cacheCommonInfo(x, sce)
-#' .refineParameters(x, sce0)
-#'
 #' # Replaces the default with something sensible.
 #' sce <- runPCA(sce)
 #' sce0 <- .cacheCommonInfo(x, sce)
@@ -54,7 +50,6 @@ setMethod("initialize", "__ENCODED__", function(.Object, ...) {
 })
 
 #' @export
-#' @importClassesFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom methods callNextMethod
 setMethod(".cacheCommonInfo", "__ENCODED__", function(x, se) {
     callNextMethod()

From a432c5db25406fa81a0ccd9055b7b5ea55c64b06 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:28:59 +0000
Subject: [PATCH 04/10] update system.file to search template in iSEEu

---
 R/addin.R                | 8 ++++----
 inst/rstudio/addins.dcf  | 2 +-
 inst/scripts/new_panel.R | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/addin.R b/R/addin.R
index 579e096..be466e4 100644
--- a/R/addin.R
+++ b/R/addin.R
@@ -1,9 +1,9 @@
 new_panel_addin = function() {
-  sys.source(system.file(package = 'iSEE', 'scripts', 'new_panel.R'))
+  sys.source(system.file(package = 'iSEEu', 'scripts', 'new_panel.R'))
 }
 
 #' @importFrom methods extends getClasses
-collect_parents <- function() {
+collect_parent_classes <- function() {
 	x <- unique(c(getClasses("package:iSEE"), getClasses("package:iSEEu")))
 	is_panel <- function(Class) {
 		extends(Class, "Panel")
@@ -29,8 +29,8 @@ collect_parents <- function() {
 #' @examples
 #' new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
 new_panel_file <- function(encoded, decoded, parent="Panel") {
-  template_file <- system.file(package = "iSEE", "templates", "NewPanel.R")
-  template_content <- scan(template_file, "character", sep = "\n", quiet = TRUE)
+  template_file <- system.file(package = "iSEEu", "templates", "NewPanel.R")
+  template_content <- scan(template_file, "character", sep = "\n", quiet = TRUE, blank.lines.skip = FALSE)
   template_content <- paste0(template_content, collapse = "\n")
   template_content <- gsub("__ENCODED__", encoded, template_content, fixed = TRUE)
   template_content <- gsub("__DECODED__", decoded, template_content, fixed = TRUE)
diff --git a/inst/rstudio/addins.dcf b/inst/rstudio/addins.dcf
index 61b68d1..e12a5d1 100644
--- a/inst/rstudio/addins.dcf
+++ b/inst/rstudio/addins.dcf
@@ -1,4 +1,4 @@
-Name: New Panel
+Name: New iSEE Panel
 Description: Create a new panel class with iSEE::new_panel().
 Binding: new_panel_addin
 Interactive: true
diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
index f465aab..a9a570e 100644
--- a/inst/scripts/new_panel.R
+++ b/inst/scripts/new_panel.R
@@ -3,7 +3,7 @@ local({
   sel_input = function(...) shiny::selectizeInput(
     ..., width = '98%', multiple = FALSE, options = list(create = TRUE)
   )
-  parent_choices = sort(iSEE:::collect_parents())
+  parent_choices = sort(iSEE:::collect_parent_classes())
   shiny::runGadget(
     miniUI::miniPage(miniUI::miniContentPanel(
       txt_input('encoded', 'Class encoded name', placeholder = 'MyNewPlot'),

From a3db5caee31b7a2d1003bdfe8e369b8075a02838 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:30:44 +0000
Subject: [PATCH 05/10] Credit where credit is due

---
 inst/scripts/new_panel.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
index a9a570e..923f5d6 100644
--- a/inst/scripts/new_panel.R
+++ b/inst/scripts/new_panel.R
@@ -1,3 +1,4 @@
+# Adapted from https://github.com/rstudio/blogdown/blob/master/inst/scripts/new_post.R
 local({
   txt_input = function(..., width = '100%') shiny::textInput(..., width = width)
   sel_input = function(...) shiny::selectizeInput(

From 410bbd5866e7be85135c227317b3d628ee126d0f Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:50:43 +0000
Subject: [PATCH 06/10] updated internal function call to iSEEu

---
 R/addin.R                | 18 ++++++++++++++++++
 inst/scripts/new_panel.R |  2 +-
 man/.gitignore           |  1 +
 3 files changed, 20 insertions(+), 1 deletion(-)
 create mode 100644 man/.gitignore

diff --git a/R/addin.R b/R/addin.R
index be466e4..18fc82b 100644
--- a/R/addin.R
+++ b/R/addin.R
@@ -1,7 +1,25 @@
+#' New iSEE panel class addin.
+#'
+#' Runs the addin miniUI to create a new iSEE panel class.
+#'
+#' @return `NULL`, invisibly.
+#'
+#' @author Kevin Rue-Albrecht
+#'
+#' @rdname INTERNAL_new_panel_addin
 new_panel_addin = function() {
   sys.source(system.file(package = 'iSEEu', 'scripts', 'new_panel.R'))
 }
 
+#' List available parent classes for new iSEE panel classes
+#'
+#' Collects the list of classes - both virtual and concrete - defined in either [iSEE::iSEE-pkg] or `iSEEu`, and that extend the [iSEE::Panel-class].
+#'
+#' @return A character vector
+#'
+#' @author Kevin Rue-Albrecht
+#'
+#' @rdname INTERNAL_collect_parent_classes
 #' @importFrom methods extends getClasses
 collect_parent_classes <- function() {
 	x <- unique(c(getClasses("package:iSEE"), getClasses("package:iSEEu")))
diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
index 923f5d6..a3e92a1 100644
--- a/inst/scripts/new_panel.R
+++ b/inst/scripts/new_panel.R
@@ -4,7 +4,7 @@ local({
   sel_input = function(...) shiny::selectizeInput(
     ..., width = '98%', multiple = FALSE, options = list(create = TRUE)
   )
-  parent_choices = sort(iSEE:::collect_parent_classes())
+  parent_choices = sort(iSEEu:::collect_parent_classes())
   shiny::runGadget(
     miniUI::miniPage(miniUI::miniContentPanel(
       txt_input('encoded', 'Class encoded name', placeholder = 'MyNewPlot'),
diff --git a/man/.gitignore b/man/.gitignore
new file mode 100644
index 0000000..b0abb65
--- /dev/null
+++ b/man/.gitignore
@@ -0,0 +1 @@
+INTERNAL_*

From 5f257d77275bc6f54ba6b38b53a9ab676fa10f66 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:51:39 +0000
Subject: [PATCH 07/10] Move another internal call from iSEE to iSEEu

---
 inst/scripts/new_panel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
index a3e92a1..3d03b5e 100644
--- a/inst/scripts/new_panel.R
+++ b/inst/scripts/new_panel.R
@@ -32,7 +32,7 @@ local({
           warning('The parent class name is empty!', call. = FALSE)
         )
 
-        iSEE:::new_panel_file(encoded, decoded, parentclass)
+        iSEEu:::new_panel_file(encoded, decoded, parentclass)
         shiny::stopApp()
       })
 

From 8c6370c627178d44c6aaf2658341706e9dd3df2a Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 19:52:47 +0000
Subject: [PATCH 08/10] restore syntax from blogdown template

---
 inst/scripts/new_panel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/scripts/new_panel.R b/inst/scripts/new_panel.R
index 3d03b5e..2c297c0 100644
--- a/inst/scripts/new_panel.R
+++ b/inst/scripts/new_panel.R
@@ -32,7 +32,7 @@ local({
           warning('The parent class name is empty!', call. = FALSE)
         )
 
-        iSEEu:::new_panel_file(encoded, decoded, parentclass)
+        iSEEu::new_panel_file(encoded, decoded, parentclass)
         shiny::stopApp()
       })
 

From a47391574de189c2fb195c6547e771150ffe642f Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 20:19:25 +0000
Subject: [PATCH 09/10] missing dependency: methods

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6dfd794..c51c292 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -31,6 +31,7 @@ Encoding: UTF-8
 Depends: 
     iSEE
 Imports:
+    methods,
     S4Vectors,
     shiny
 Suggests: 

From a5750ce2327cd86b74011fbabcd661ed845687d2 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 13 Dec 2019 22:16:44 +0000
Subject: [PATCH 10/10] Run example in RStudio only

---
 R/addin.R             | 8 +++++---
 man/new_panel_file.Rd | 6 ++++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/addin.R b/R/addin.R
index 18fc82b..7004b11 100644
--- a/R/addin.R
+++ b/R/addin.R
@@ -15,7 +15,7 @@ new_panel_addin = function() {
 #'
 #' Collects the list of classes - both virtual and concrete - defined in either [iSEE::iSEE-pkg] or `iSEEu`, and that extend the [iSEE::Panel-class].
 #'
-#' @return A character vector
+#' @return A character vector of S4 class names.
 #'
 #' @author Kevin Rue-Albrecht
 #'
@@ -30,7 +30,7 @@ collect_parent_classes <- function() {
 	x[keep]
 }
 
-#' Create a new panel file
+#' Create a new panel class file
 #'
 #' Opens a template R script in the editor, to define a new iSEE panel class .
 #'
@@ -45,7 +45,9 @@ collect_parent_classes <- function() {
 #' @seealso \linkS4class{Panel}
 #'
 #' @examples
-#' new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+#' if (Sys.getenv("RSTUDIO") == "1") {
+#'     new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+#' }
 new_panel_file <- function(encoded, decoded, parent="Panel") {
   template_file <- system.file(package = "iSEEu", "templates", "NewPanel.R")
   template_content <- scan(template_file, "character", sep = "\n", quiet = TRUE, blank.lines.skip = FALSE)
diff --git a/man/new_panel_file.Rd b/man/new_panel_file.Rd
index 290fe9a..7904165 100644
--- a/man/new_panel_file.Rd
+++ b/man/new_panel_file.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/addin.R
 \name{new_panel_file}
 \alias{new_panel_file}
-\title{Create a new panel file}
+\title{Create a new panel class file}
 \usage{
 new_panel_file(encoded, decoded, parent = "Panel")
 }
@@ -17,7 +17,9 @@ new_panel_file(encoded, decoded, parent = "Panel")
 Opens a template R script in the editor, to define a new iSEE panel class .
 }
 \examples{
-new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+if (Sys.getenv("RSTUDIO") == "1") {
+    new_panel_file("NewRedDimPlot", "New reduced dimension plot", "RedDimPlot")
+}
 }
 \seealso{
 \linkS4class{Panel}