Fix tests

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: iSEEtree
-Version: 0.99.0
+Version: 0.99.1
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "[email protected]",
@@ -15,12 +15,13 @@ Description:
     TreeSummarizedExperiment objects. Not surprisingly, it also depends on the
     generic panels from iSEE.
 biocViews: Microbiome, Software, Visualization, DataImport
-License: Artistic-2.0
+License: Artistic-2.0 + file LICENSE
 Encoding: UTF-8
 Depends:
     R (>= 4.0),
     iSEE
 Imports:
+    grDevices,
     methods,
     miaViz,
     S4Vectors,
@@ -29,7 +30,8 @@ Imports:
     shinyWidgets,
     SingleCellExperiment,
     SummarizedExperiment,
-    TreeSummarizedExperiment
+    TreeSummarizedExperiment,
+    utils
 Suggests:
     BiocStyle,
     knitr,
@@ -38,7 +40,6 @@ Suggests:
     rmarkdown,
     scater,
     testthat (>= 3.0.0),
-    utils,
     vegan
 URL: https://github.com/microbiome/iSEEtree
 BugReports: https://github.com/microbiome/iSEEtree/issues

R/class-RDAPlot.R

@@ -110,7 +110,7 @@ setMethod("initialize", "RDAPlot", function(.Object, ...) {
     args <- .emptyDefault(args, "colour_by", NA_character_)
     args <- .emptyDefault(args, "add.vectors", TRUE)
     args <- .emptyDefault(args, "vec.text", TRUE)
-    args <- .emptyDefault(args, "visual_parameters", "None")
+    args <- .emptyDefault(args, "visual_parameters", NA_character_)
     args <- .emptyDefault(args, "add.expl.var", TRUE)
     args <- .emptyDefault(args, "add.significance", TRUE)
     args <- .emptyDefault(args, "ellipse.alpha", 0.2)
@@ -301,11 +301,12 @@ setMethod(".definePanelTour", "RDAPlot", function(x) {
     callNextMethod())
 })
 
+#' @importFrom SummarizedExperiment colData
+#' @importFrom grDevices rainbow
+#' @importFrom methods slot
 #' @importFrom iSEE .getEncodedName .selectInput.iSEE .checkboxInput.iSEE .sliderInput.iSEE
 #'   .conditionalOnCheckSolo .checkboxGroupInput.iSEE .conditionalOnCheckGroup
 #'   .numericInput.iSEE
-#' @importFrom methods slot
-#' @importFrom SummarizedExperiment colData
 .create_visual_box_for_rda <- function(x, se) {
     panel_name <- .getEncodedName(x)
 
@@ -382,7 +383,6 @@ setMethod(".definePanelTour", "RDAPlot", function(x) {
             "_visual_parameters"), intro = "Here, we can choose
             the visual parameters to adjust")))})
 
-
     # Define what parameters the user can adjust
     collapseBox(paste0(panel_name, "_Visual"),
         title="Visual parameters", open=FALSE,

R/class-RowTreePlot.R

@@ -98,10 +98,10 @@ setMethod("initialize", "RowTreePlot", function(.Object, ...) {
     args <- .emptyDefault(args, "node_colour_by", NA_character_)
     args <- .emptyDefault(args, "node_size_by", NA_character_)
     args <- .emptyDefault(args, "node_shape_by", NA_character_)
-    args <- .emptyDefault(args, "visual_parameters", "None")
-    args <- .emptyDefault(args, "colour_parameters", "None")
-    args <- .emptyDefault(args, "shape_parameters", "None")
-    args <- .emptyDefault(args, "size_parameters", "None")
+    args <- .emptyDefault(args, "visual_parameters", NA_character_)
+    args <- .emptyDefault(args, "colour_parameters", NA_character_)
+    args <- .emptyDefault(args, "shape_parameters", NA_character_)
+    args <- .emptyDefault(args, "size_parameters", NA_character_)
     args <- .emptyDefault(args, "order_tree", FALSE)
 
     do.call(callNextMethod, c(list(.Object), args))

tests/testthat/test-RDAPlot.R

@@ -16,8 +16,9 @@ test_that("RDAPlot", {
 
   expect_s3_class(.defineOutput(panel), "shiny.tag.list")
   expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
-  'p <- miaViz::plotRDA(se, dimred="RDA", colour_by="ClinicalStatus",
-    confidence.level=0.95, add.expl.var=TRUE, add.significance=TRUE)', fixed = TRUE)
+  'p <- miaViz::plotRDA(se, dimred="RDA", colour_by="ClinicalStatus",\n    ',
+  'confidence.level=0.95, add.expl.var=TRUE, add.significance=TRUE)',
+  fixed = TRUE)
 
   expect_true(.hideInterface(panel, "RowSelectionSource"))
   expect_false(.multiSelectionResponsive(panel, "row"))