From 7751de19cedc4a431d7653b06045499fa7679209 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:09:57 +0100
Subject: [PATCH] docs: moves roxygen2 template to folder inside man page
 according to documentation

---
 .Rbuildignore                              | 2 +-
 man-roxygen/ggplot2_args_multi.R           | 7 -------
 man/roxygen/templates/ggplot2_args_multi.R | 8 ++++++++
 man/tm_a_pca.Rd                            | 5 +++--
 man/tm_a_regression.Rd                     | 5 +++--
 man/tm_g_association.Rd                    | 5 +++--
 man/tm_g_distribution.Rd                   | 5 +++--
 man/tm_missing_data.Rd                     | 5 +++--
 man/tm_outliers.Rd                         | 5 +++--
 9 files changed, 27 insertions(+), 20 deletions(-)
 delete mode 100644 man-roxygen/ggplot2_args_multi.R
 create mode 100644 man/roxygen/templates/ggplot2_args_multi.R

diff --git a/.Rbuildignore b/.Rbuildignore
index 08f35f406..bc51aef0c 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -28,7 +28,7 @@ SECURITY.md
 ^Jenkinsfile$
 ^logs$
 ^Makefile$
-^man-roxygen$
+^man/roxygen$
 ^Meta$
 ^outputdir$
 ^scratch$
diff --git a/man-roxygen/ggplot2_args_multi.R b/man-roxygen/ggplot2_args_multi.R
deleted file mode 100644
index 332f0084d..000000000
--- a/man-roxygen/ggplot2_args_multi.R
+++ /dev/null
@@ -1,7 +0,0 @@
-#' @param ggplot2_args optional, (`ggplot2_args`) object created by [`teal.widgets::ggplot2_args()`]
-#'  with settings for all the plots or named list of `ggplot2_args` objects for plot-specific settings.
-#'  The argument is merged with options variable `teal.ggplot2_args` and default module setup.
-#'
-#'  List names should match the following: `c("default", <%=ggnames%>)`.
-#'
-#'  For more details see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.
diff --git a/man/roxygen/templates/ggplot2_args_multi.R b/man/roxygen/templates/ggplot2_args_multi.R
new file mode 100644
index 000000000..466c9a2fa
--- /dev/null
+++ b/man/roxygen/templates/ggplot2_args_multi.R
@@ -0,0 +1,8 @@
+#' @param ggplot2_args (`ggplot2_args` or `named list` of `ggplot2_args`s) optional.
+#' Object created by [`teal.widgets::ggplot2_args()`] and contains settings for all the plots,
+#' or is a named `list` of `ggplot2_args` objects for plot-specific settings.
+#' The argument is merged with options variable `teal.ggplot2_args` and default module setup.
+#'
+#' List names should match the following: `c("default", <%=ggnames%>)`.
+#'
+#' For more details see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.
diff --git a/man/tm_a_pca.Rd b/man/tm_a_pca.Rd
index fd9a063e7..bab605de6 100644
--- a/man/tm_a_pca.Rd
+++ b/man/tm_a_pca.Rd
@@ -34,8 +34,9 @@ specifying columns used to compute PCA.}
 
 \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \code{c("default", "Elbow plot", "Circle plot", "Biplot", "Eigenvector plot")}.
diff --git a/man/tm_a_regression.Rd b/man/tm_a_regression.Rd
index 5d539d163..67f41ab39 100644
--- a/man/tm_a_regression.Rd
+++ b/man/tm_a_regression.Rd
@@ -52,8 +52,9 @@ vector of \code{value}, \code{min}, and \code{max}.
 
 \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \verb{c("default", "Response vs Regressor", "Residuals vs Fitted", "Scale-Location", "Cook's distance", "Residuals vs Leverage"", "Cook's dist vs Leverage")}.
diff --git a/man/tm_g_association.Rd b/man/tm_g_association.Rd
index aa851556a..1a77b2165 100644
--- a/man/tm_g_association.Rd
+++ b/man/tm_g_association.Rd
@@ -50,8 +50,9 @@ with text placed before the output to put the output into context. For example a
 \item{post_output}{(\code{shiny.tag}, optional) Text or UI element to be displayed after the module's output,
 adding context or further instructions. Elements like \code{shiny::helpText()} are useful.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \code{c("default", "Bivariate1", "Bivariate2")}.
diff --git a/man/tm_g_distribution.Rd b/man/tm_g_distribution.Rd
index a04c07016..b0d4158f9 100644
--- a/man/tm_g_distribution.Rd
+++ b/man/tm_g_distribution.Rd
@@ -37,8 +37,9 @@ Defaults to density (\code{FALSE}).}
 
 \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \code{c("default", "Histogram", "QQplot")}.
diff --git a/man/tm_missing_data.Rd b/man/tm_missing_data.Rd
index e94ed9dfe..4448b8358 100644
--- a/man/tm_missing_data.Rd
+++ b/man/tm_missing_data.Rd
@@ -33,8 +33,9 @@ ignored.}
 
 \item{ggtheme}{(\code{character}, optional) Specifies the default \code{ggplot2} theme for plots. Defaults to \code{classic}.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \code{c("default", "Summary Obs", "Summary Patients", "Combinations Main", "Combinations Hist", "By Subject")}.
diff --git a/man/tm_outliers.Rd b/man/tm_outliers.Rd
index 9bda163f3..a057bc1ee 100644
--- a/man/tm_outliers.Rd
+++ b/man/tm_outliers.Rd
@@ -28,8 +28,9 @@ Specifies the categorical variable(s) to split the selected outlier variables on
 
 \item{ggtheme}{optional, (\code{character}) \code{ggplot2} theme to be used by default. Defaults to \code{"gray"}.}
 
-\item{ggplot2_args}{optional, (\code{ggplot2_args}) object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}}
-with settings for all the plots or named list of \code{ggplot2_args} objects for plot-specific settings.
+\item{ggplot2_args}{(\code{ggplot2_args} or \verb{named list} of \code{ggplot2_args}s) optional.
+Object created by \code{\link[teal.widgets:ggplot2_args]{teal.widgets::ggplot2_args()}} and contains settings for all the plots,
+or is a named \code{list} of \code{ggplot2_args} objects for plot-specific settings.
 The argument is merged with options variable \code{teal.ggplot2_args} and default module setup.
 
 List names should match the following: \code{c("default", "Boxplot","Density Plot","Cumulative Distribution Plot")}.