chore: move code around

drieslab · Aug 15, 2024 · 1be673b · 1be673b
1 parent 55badc7
commit 1be673b
Showing 1 changed file with 134 additions and 122 deletions.
diff --git a/R/aux_save.R b/R/aux_save.R
@@ -34,10 +34,17 @@ NULL
 
 
 
-#' @describeIn plot_save (internal) ggplot saving. ...
-#' passes to cowplot::save_plot
-#' @keywords internal
-.ggplot_save_function <- function(gobject,
+
+
+#' @rdname plot_save
+#' @examples
+#' g <- GiottoClass::createGiottoInstructions(save_plot = TRUE)
+#' df <- data.frame(x = rnorm(5), y = rnorm(5))
+#' g_plot <- ggplot2::ggplot(df, ggplot2::aes(x,y)) + ggplot2::geom_point()
+#' all_plots_save_function(g, g_plot)
+#'
+#' @export
+all_plots_save_function <- function(gobject,
     plot_object,
     save_dir = NULL,
     save_folder = NULL,
@@ -56,6 +63,127 @@ NULL
     limitsize = TRUE,
     plot_count = NULL,
     ...) {
+    if (any("ggplot" %in% class(plot_object))) {
+        .ggplot_save_function(
+            gobject = gobject,
+            plot_object = plot_object,
+            save_dir = save_dir,
+            save_folder = save_folder,
+            save_name = save_name,
+            default_save_name = default_save_name,
+            save_format = save_format,
+            show_saved_plot = show_saved_plot,
+            ncol = ncol,
+            nrow = nrow,
+            scale = scale,
+            base_width = base_width,
+            base_height = base_height,
+            base_aspect_ratio = base_aspect_ratio,
+            units = units,
+            dpi = dpi,
+            limitsize = limitsize,
+            plot_count = plot_count,
+            ...
+        )
+    } else {
+        .general_save_function(
+            gobject = gobject,
+            plot_object = plot_object,
+            save_dir = save_dir,
+            save_folder = save_folder,
+            save_name = save_name,
+            default_save_name = default_save_name,
+            save_format = save_format,
+            show_saved_plot = show_saved_plot,
+            base_width = base_width,
+            base_height = base_height,
+            base_aspect_ratio = base_aspect_ratio,
+            units = units,
+            dpi = dpi,
+            plot_count = plot_count,
+            ...
+        )
+    }
+}
+
+
+
+
+#' @title showSaveParameters
+#' @name showSaveParameters
+#' @description Description of Giotto saving options,
+#' links to \code{\link{all_plots_save_function}}
+#' @returns Instructions on how to use the automatic plot saving options
+#' within Giotto
+#' @export
+#' @examples
+#' showSaveParameters()
+showSaveParameters <- function() {
+    message("This is a simple guide to help you automatically saving plots. \n")
+    message("Importantly, defaults for all these parameters can be set at
+    the beginning with createGiottoInstructions() \n")
+    message("See
+    https://rubd.github.io/Giotto/articles/instructions_and_plotting.html
+    for more information and examples \n \n")
+
+    message("Each plotting function in Giotto has 4 important parameters for
+    showing and/or saving a plot: \n
+        - show_plot: TRUE or FALSE, show the plot to the console
+        - return_plot: TRUE or FALSE, return the plot to the console
+        (e.g. to further modify or save the plot
+        - save_plot: TRUE or FALSE, automatically save the plot
+        - save_param: a list of parameters that can be set \n")
+
+    message("The following list of parameters can be provided to save_param: \n
+        - save_dir: directory to save the plot to
+        - save_folder: if not NULL, a subfolder within save_dir that will
+        be created to save the plot to
+        - save_name: name of the plot (no extension needed, see save_format)
+        - save_format: picture format to use, default is .png
+        - ncol: number of columns for multiplots
+        - nrow: number of rows for multiplot
+        - scale: scale of plots
+        - base_width: width of plot
+        - base_height: height of plot
+        - base_aspect_ratio: ratio of plot
+        - units: plotting units (e.g. in)
+        - dpi: dpi for each plot if plot is in raster format\n")
+
+    message("Example: \n
+        plotfunction(...,
+                    save_plot = TRUE,
+                    save_param = list(save_name = 'favorite_name',
+                    units = 'png'))")
+}
+
+
+
+
+# internals ####
+
+
+#' @describeIn plot_save (internal) ggplot saving. ...
+#' passes to cowplot::save_plot
+#' @keywords internal
+.ggplot_save_function <- function(gobject,
+                                  plot_object,
+                                  save_dir = NULL,
+                                  save_folder = NULL,
+                                  save_name = NULL,
+                                  default_save_name = "giotto_plot",
+                                  save_format = NULL,
+                                  show_saved_plot = FALSE,
+                                  ncol = 1,
+                                  nrow = 1,
+                                  scale = 1,
+                                  base_width = NULL,
+                                  base_height = NULL,
+                                  base_aspect_ratio = NULL,
+                                  units = NULL,
+                                  dpi = NULL,
+                                  limitsize = TRUE,
+                                  plot_count = NULL,
+                                  ...) {
     if (is.null(plot_object)) {
         stop("\t there is no object to plot \t")
     }
@@ -159,7 +287,7 @@ NULL
         stop("\t there is no object to plot \t")
     }
     save_format <- match.arg(save_format,
-        choices = c("png", "tiff", "pdf", "svg")
+                             choices = c("png", "tiff", "pdf", "svg")
     )
 
     if (any("plotly" %in% class(plot_object))) {
@@ -202,7 +330,7 @@ NULL
 
     if (any("plotly" %in% class(plot_object))) {
         htmlwidgets::saveWidget(plotly::as_widget(plot_object),
-            file = full_location
+                                file = full_location
         )
     } else {
         if (save_format == "png") {
@@ -267,122 +395,6 @@ NULL
     }
 }
 
-#' @rdname plot_save
-#' @examples
-#' g <- GiottoClass::createGiottoInstructions(save_plot = TRUE)
-#' df <- data.frame(x = rnorm(5), y = rnorm(5))
-#' g_plot <- ggplot2::ggplot(df, ggplot2::aes(x,y)) + ggplot2::geom_point()
-#' all_plots_save_function(g, g_plot)
-#'
-#' @export
-all_plots_save_function <- function(gobject,
-    plot_object,
-    save_dir = NULL,
-    save_folder = NULL,
-    save_name = NULL,
-    default_save_name = "giotto_plot",
-    save_format = NULL,
-    show_saved_plot = FALSE,
-    ncol = 1,
-    nrow = 1,
-    scale = 1,
-    base_width = NULL,
-    base_height = NULL,
-    base_aspect_ratio = NULL,
-    units = NULL,
-    dpi = NULL,
-    limitsize = TRUE,
-    plot_count = NULL,
-    ...) {
-    if (any("ggplot" %in% class(plot_object))) {
-        .ggplot_save_function(
-            gobject = gobject,
-            plot_object = plot_object,
-            save_dir = save_dir,
-            save_folder = save_folder,
-            save_name = save_name,
-            default_save_name = default_save_name,
-            save_format = save_format,
-            show_saved_plot = show_saved_plot,
-            ncol = ncol,
-            nrow = nrow,
-            scale = scale,
-            base_width = base_width,
-            base_height = base_height,
-            base_aspect_ratio = base_aspect_ratio,
-            units = units,
-            dpi = dpi,
-            limitsize = limitsize,
-            plot_count = plot_count,
-            ...
-        )
-    } else {
-        .general_save_function(
-            gobject = gobject,
-            plot_object = plot_object,
-            save_dir = save_dir,
-            save_folder = save_folder,
-            save_name = save_name,
-            default_save_name = default_save_name,
-            save_format = save_format,
-            show_saved_plot = show_saved_plot,
-            base_width = base_width,
-            base_height = base_height,
-            base_aspect_ratio = base_aspect_ratio,
-            units = units,
-            dpi = dpi,
-            plot_count = plot_count,
-            ...
-        )
-    }
-}
-
-
-
-
-#' @title showSaveParameters
-#' @name showSaveParameters
-#' @description Description of Giotto saving options,
-#' links to \code{\link{all_plots_save_function}}
-#' @returns Instructions on how to use the automatic plot saving options
-#' within Giotto
-#' @export
-#' @examples
-#' showSaveParameters()
-showSaveParameters <- function() {
-    message("This is a simple guide to help you automatically saving plots. \n")
-    message("Importantly, defaults for all these parameters can be set at
-    the beginning with createGiottoInstructions() \n")
-    message("See
-    https://rubd.github.io/Giotto/articles/instructions_and_plotting.html
-    for more information and examples \n \n")
 
-    message("Each plotting function in Giotto has 4 important parameters for
-    showing and/or saving a plot: \n
-        - show_plot: TRUE or FALSE, show the plot to the console
-        - return_plot: TRUE or FALSE, return the plot to the console
-        (e.g. to further modify or save the plot
-        - save_plot: TRUE or FALSE, automatically save the plot
-        - save_param: a list of parameters that can be set \n")
 
-    message("The following list of parameters can be provided to save_param: \n
-        - save_dir: directory to save the plot to
-        - save_folder: if not NULL, a subfolder within save_dir that will
-        be created to save the plot to
-        - save_name: name of the plot (no extension needed, see save_format)
-        - save_format: picture format to use, default is .png
-        - ncol: number of columns for multiplots
-        - nrow: number of rows for multiplot
-        - scale: scale of plots
-        - base_width: width of plot
-        - base_height: height of plot
-        - base_aspect_ratio: ratio of plot
-        - units: plotting units (e.g. in)
-        - dpi: dpi for each plot if plot is in raster format\n")
 
-    message("Example: \n
-        plotfunction(...,
-                    save_plot = TRUE,
-                    save_param = list(save_name = 'favorite_name',
-                    units = 'png'))")
-}