Updated documentation & tests also removed iSEE::: calls

microbiome · Jun 13, 2024 · 9a0a7ad · 9a0a7ad
1 parent d41c306
commit 9a0a7ad
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Showing 4 changed files with 16 additions and 9 deletions.
diff --git a/R/class-AbundanceDensityPlot.R b/R/class-AbundanceDensityPlot.R
@@ -340,7 +340,7 @@ setMethod(".definePanelTour", "AbundanceDensityPlot", function(x) {
                 selected=slot(x, "dots_colour")),
             .conditionalOnRadio(
                 paste0(panel_name, "_dots_colour"), "Column data",
-                iSEE:::.selectInputHidden(x, field="dots_colour_by",
-                    label="Color dots by", choices=names(colData(se)), 
-                    selected=slot(x, "dots_colour_by"))))
+                    .selectInput.iSEE(x, field="dots_colour_by",
+                        label="Color dots by", choices=names(colData(se)), 
+                        selected=slot(x, "dots_colour_by"))))
 }
diff --git a/R/class-AbundancePlot.R b/R/class-AbundancePlot.R
@@ -90,14 +90,14 @@ setMethod(".defineDataInterface", "AbundancePlot", function(x, se, select_info)
         .conditionalOnRadio(
             paste0(panel_name, "_order_sample"), "Column data",
             list(
-                iSEE:::.selectInputHidden(x, field="order_sample_by",
+                .selectInput.iSEE(x, field="order_sample_by",
                     label="Order sample by", choices=names(colData(se)), 
                     selected=slot(x, "order_sample_by")),
-                iSEE:::.checkboxInputHidden(x, field="decreasing",
+                .checkboxInput.iSEE(x, field="decreasing",
                     label="Order decreasingly", value=slot(x, "decreasing")))),
         .conditionalOnRadio(
             paste0(panel_name, "_order_sample"), "Row data",
-            iSEE:::.selectInputHidden(x, field="order_sample_by",
+                .selectInput.iSEE(x, field="order_sample_by",
                     label="Order sample by", choices=unique(rowData(se)$Phylum), 
                     selected=slot(x, "order_sample_by"))))
 })

diff --git a/man/RDAPlot.Rd b/man/RDAPlot.Rd
diff --git a/tests/testthat/test-RDAPlot.R b/tests/testthat/test-RDAPlot.R
@@ -16,9 +16,8 @@ test_that("RDAPlot", {
 
   expect_s3_class(.defineOutput(panel), "shiny.tag.list")
   expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
-  'p <- miaViz::plotRDA(se, dimred="RDA", add.ellipse="fill",\n    colour_by=',
-  '"ClinicalStatus", vec.text=TRUE, add.vectors=TRUE, confidence.level=0.95,
-  ellipse.alpha = 0.2, add.significance=TRUE, add.expl.var=TRUE)', fixed = TRUE)
+  'p <- miaViz::plotRDA(se, dimred="RDA", colour_by="ClinicalStatus",
+    confidence.level=0.95, add.expl.var=TRUE, add.significance=TRUE)', fixed = TRUE)
 
   expect_true(.hideInterface(panel, "RowSelectionSource"))
   expect_false(.multiSelectionResponsive(panel, "row"))