Do not export .generateOutput

microbiome · Jun 28, 2024 · 7eab2ab · 7eab2ab
1 parent cf5ae83
commit 7eab2ab
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Showing 5 changed files with 27 additions and 16 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -62,7 +62,6 @@ importFrom(shiny,plotOutput)
 importFrom(shiny,renderPlot)
 importFrom(shinyWidgets,addSpinner)
 importFrom(utils,stack)
-importMethodsFrom(iSEE,.exportOutput)
 importMethodsFrom(iSEE,.generateOutput)
 importMethodsFrom(iSEE,.panelColor)
 importMethodsFrom(iSEE,.renderOutput)
diff --git a/R/class-AbundanceDensityPlot.R b/R/class-AbundanceDensityPlot.R
@@ -236,15 +236,18 @@ setMethod(".renderOutput", "AbundanceDensityPlot",
     callNextMethod()
 })
 
-#' @export
 #' @importFrom grDevices pdf dev.off
 setMethod(".exportOutput", "AbundanceDensityPlot",
     function(x, se, all_memory, all_contents) {
 
-    contents <- .generateOutput(x, se, all_memory=all_memory, all_contents=all_contents)
+    contents <- .generateOutput(x, se, all_memory=all_memory,
+        all_contents=all_contents)
+
     newpath <- paste0(.getEncodedName(x), ".pdf")
 
-    pdf(newpath, width=slot(x, "PanelHeight")/75, height=slot(x, "PanelWidth")*2)
+    pdf(newpath, width=slot(x, "PanelHeight") / 75,
+        height=slot(x, "PanelWidth") * 2)
+
     print(contents$plot)
     dev.off()
 

diff --git a/R/class-AbundancePlot.R b/R/class-AbundancePlot.R
@@ -205,15 +205,18 @@ setMethod(".renderOutput", "AbundancePlot",
     callNextMethod()
 })
 
-#' @export
 #' @importFrom grDevices pdf dev.off
 setMethod(".exportOutput", "AbundancePlot",
     function(x, se, all_memory, all_contents) {
 
-    contents <- .generateOutput(x, se, all_memory=all_memory, all_contents=all_contents)
+    contents <- .generateOutput(x, se, all_memory=all_memory,
+        all_contents=all_contents)
+
     newpath <- paste0(.getEncodedName(x), ".pdf")
 
-    pdf(newpath, width=slot(x, "PanelHeight")/75, height=slot(x, "PanelWidth")*2)
+    pdf(newpath, width=slot(x, "PanelHeight") / 75,
+        height=slot(x, "PanelWidth") * 2)
+
     print(contents$plot)
     dev.off()
 

diff --git a/R/class-RDAPlot.R b/R/class-RDAPlot.R
@@ -264,15 +264,18 @@ setMethod(".renderOutput", "RDAPlot",
     callNextMethod()
 })
 
-#' @export
 #' @importFrom grDevices pdf dev.off
 setMethod(".exportOutput", "RDAPlot",
     function(x, se, all_memory, all_contents) {
 
-    contents <- .generateOutput(x, se, all_memory=all_memory, all_contents=all_contents)
+    contents <- .generateOutput(x, se, all_memory=all_memory,
+        all_contents=all_contents)
+
     newpath <- paste0(.getEncodedName(x), ".pdf")
 
-    pdf(newpath, width=slot(x, "PanelHeight")/75, height=slot(x, "PanelWidth")*2)
+    pdf(newpath, width=slot(x, "PanelHeight") / 75,
+        height=slot(x, "PanelWidth") * 2)
+
     print(contents$plot)
     dev.off()
 

diff --git a/R/class-RowTreePlot.R b/R/class-RowTreePlot.R
@@ -232,18 +232,21 @@ setMethod(".renderOutput", "RowTreePlot",
     callNextMethod()
 })
 
-#' @export
 #' @importFrom grDevices pdf dev.off
 setMethod(".exportOutput", "RowTreePlot",
     function(x, se, all_memory, all_contents) {
-
-    contents <- .generateOutput(x, se, all_memory=all_memory, all_contents=all_contents)
+
+    contents <- .generateOutput(x, se, all_memory=all_memory,
+        all_contents=all_contents)
+
     newpath <- paste0(.getEncodedName(x), ".pdf")
-
-    pdf(newpath, width=slot(x, "PanelHeight")/75, height=slot(x, "PanelWidth")*2)
+
+    pdf(newpath, width=slot(x, "PanelHeight") / 75,
+        height=slot(x, "PanelWidth") * 2)
+
     print(contents$plot)
     dev.off()
-
+            
     newpath
 })