Fix checks

microbiome · Apr 30, 2024 · bf13c9e · bf13c9e
1 parent 528f4db
commit bf13c9e
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,8 +9,6 @@ exportClasses(AbundanceDensityPlot)
 exportClasses(AbundancePlot)
 exportClasses(RDAPlot)
 exportClasses(RowTreePlot)
-exportMethods(.multiSelectionDimension)
-exportMethods(.multiSelectionRestricted)
 exportMethods(iSEE)
 importFrom(S4Vectors,isEmpty)
 importFrom(S4Vectors,setValidity2)
@@ -27,6 +25,7 @@ importFrom(iSEE,.checkboxInput.iSEE)
 importFrom(iSEE,.conditionalOnCheckSolo)
 importFrom(iSEE,.conditionalOnRadio)
 importFrom(iSEE,.createProtectedParameterObservers)
+importFrom(iSEE,.createUnprotectedParameterObservers)
 importFrom(iSEE,.emptyDefault)
 importFrom(iSEE,.getEncodedName)
 importFrom(iSEE,.getPanelColor)
@@ -54,4 +53,5 @@ importFrom(shiny,renderPlot)
 importFrom(shinyWidgets,addSpinner)
 importMethodsFrom(iSEE,.createObservers)
 importMethodsFrom(iSEE,.generateOutput)
+importMethodsFrom(iSEE,.panelColor)
 importMethodsFrom(iSEE,.renderOutput)
diff --git a/R/class-AbundanceDensityPlot.R b/R/class-AbundanceDensityPlot.R
@@ -121,6 +121,7 @@ setMethod(".defineInterface", "AbundanceDensityPlot", function(x, se, select_inf
 })
 
 #' @importFrom iSEE .getEncodedName .createProtectedParameterObservers
+#'   .createUnprotectedParameterObservers
 setMethod(".createObservers", "AbundanceDensityPlot", function(x, se, input, session, pObjects, rObjects) {
   callNextMethod()
 
@@ -143,6 +144,7 @@ setMethod(".createObservers", "AbundanceDensityPlot", function(x, se, input, ses
 
 setMethod(".fullName", "AbundanceDensityPlot", function(x) "Abundance density plot")
 
+#' @importMethodsFrom iSEE .panelColor
 setMethod(".panelColor", "AbundanceDensityPlot", function(x) "#8B5A2B")
 
 #' @importFrom iSEE .getEncodedName
@@ -216,10 +218,8 @@ setMethod(".hideInterface", "AbundanceDensityPlot", function(x, field) {
   }
 })
 
-#' @export
 setMethod(".multiSelectionDimension", "AbundanceDensityPlot", function(x) "row")
 
-#' @export
 setMethod(".multiSelectionRestricted", "AbundanceDensityPlot", function(x) {
   slot(x, "RowSelectionRestrict")
 })

diff --git a/R/class-RowTreePlot.R b/R/class-RowTreePlot.R
@@ -106,6 +106,7 @@ setMethod(".defineInterface", "RowTreePlot", function(x, se, select_info) {
 })
 
 #' @importFrom iSEE .getEncodedName .createProtectedParameterObservers
+#'   .createUnprotectedParameterObservers
 setMethod(".createObservers", "RowTreePlot", function(x, se, input, session, pObjects, rObjects) {
   callNextMethod()
 
@@ -128,6 +129,7 @@ setMethod(".createObservers", "RowTreePlot", function(x, se, input, session, pOb
 
 setMethod(".fullName", "RowTreePlot", function(x) "Row tree plot")
 
+#' @importMethodsFrom iSEE .panelColor
 setMethod(".panelColor", "RowTreePlot", function(x) "#4EEE94")
 
 #' @importFrom iSEE .getEncodedName

diff --git a/vignettes/iSEEtree.Rmd b/vignettes/iSEEtree.Rmd
@@ -110,7 +110,7 @@ tse <- GlobalPatterns
 
 # Agglomerate TreeSE by Genus
 tse_genus <- mergeFeaturesByRank(tse,
-                                 rank = "Genus",
+                                 rank = "Order",
                                  onRankOnly = TRUE)
 
 # Add relabundance assay
@@ -121,7 +121,7 @@ tse_genus <- scater::runPCA(tse_genus, assay.type = "counts")
 
 # Launch iSEE
 if (interactive()) {
-  iSEE(tse_genus)
+  iSEE(tse_genus, initial = c(ColumnDataTable(), ComplexHeatmapPlot(), AbundanceDensityPlot()))
 }
 ```