Add unit tests for new panels

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: iSEEtree
-Version: 1.3.1
+Version: 1.3.2
 Authors@R: 
     c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"),
            email = "giulio.benedetti@utu.fi",

tests/testthat/test-ColumnGraphPlot.R

@@ -0,0 +1,52 @@
+test_that("ColumnGraphPlot", {
+
+  output <- new.env()
+  pObjects <- new.env()
+  rObjects <- new.env()
+  select_info <- list(single = list(feature = "---", sample = "---"),
+                      multi = list(row = "---", column = "---"))
+
+  data("GlobalPatterns", package = "mia")
+  tse <- GlobalPatterns
+
+  data("col_graph", package = "miaViz")
+  metadata(tse)$graph <- col_graph
+
+  panel <- ColumnGraphPlot()
+
+  panel[["layout"]] <- "kk"
+
+  expect_identical(.getEncodedName(panel), "ColumnGraphPlotNA")
+  expect_identical(.fullName(panel), "Column graph plot")
+  expect_identical(.panelColor(panel), "purple")
+
+  expect_s3_class(.defineInterface(panel, tse, select_info)[[1]][[1]], "shiny.tag.list")
+  expect_length(.defineDataInterface(panel, tse, select_info), 3)
+
+  expect_s3_class(.defineOutput(panel), "shiny.tag.list")
+  expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
+      'p <- miaViz::plotColGraph(se, name=\"graph\", assay.type=\"counts\",\n    show.label=FALSE, layout=\"kk\", edge.type=\"fan\", add.legend=TRUE)',
+      fixed = TRUE)
+
+  expect_true(.hideInterface(panel, "ColumnSelectionSource"))
+  expect_false(.multiSelectionResponsive(panel, "row"))
+  expect_true(.multiSelectionResponsive(panel, "column"))
+
+  expect_contains(slotNames(panel), c("name", "assay.type", "layout",
+      "show.label", "add.legend", "edge.colour.by", "edge.size.by",
+      "node.colour.by", "node.shape.by", "node.size.by"))
+
+  expect_contains(.definePanelTour(panel)[[1]],
+      c("#ColumnGraphPlotNA_DataBoxOpen", "#ColumnGraphPlotNA_VisualBoxOpen",
+      "#ColumnGraphPlotNA", "#ColumnGraphPlotNA_SelectionBoxOpen"))
+
+  expect_s3_class(.create_visual_box_for_graph(panel, tse), "shiny.tag.list")
+
+  expect_null(.renderOutput(panel, tse, output = output, pObjects = pObjects, rObjects = rObjects))
+  expect_s3_class(output$ColumnGraphPlotNA, "shiny.render.function")
+  expect_s3_class(output$ColumnGraphPlotNA_INTERNAL_PanelMultiSelectInfo, "shiny.render.function")
+  expect_s3_class(output$ColumnGraphPlotNA_INTERNAL_PanelSelectLinkInfo, "shiny.render.function")
+
+  expect_identical(.exportOutput(panel, tse), "ColumnGraphPlotNA.pdf")
+
+})

tests/testthat/test-PrevalencePlot.R

@@ -0,0 +1,48 @@
+test_that("PrevalencePlot", {
+
+  output <- new.env()
+  pObjects <- new.env()
+  rObjects <- new.env()
+  select_info <- list(single = list(feature = "---", sample = "---"),
+                      multi = list(row = "---", column = "---"))
+
+  data("Tengeler2020", package = "mia")
+  tse <- Tengeler2020
+
+  panel <- PrevalencePlot()
+
+  panel[["include.lowest"]] <- TRUE
+
+  expect_identical(.getEncodedName(panel), "PrevalencePlotNA")
+  expect_identical(.fullName(panel), "Prevalence plot")
+  expect_identical(.panelColor(panel), "grey")
+
+  expect_s3_class(.defineInterface(panel, tse, select_info)[[1]][[1]], "shiny.tag.list")
+  expect_length(.defineDataInterface(panel, tse, select_info), 6)
+
+  expect_s3_class(.defineOutput(panel), "shiny.tag.list")
+  # expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
+  #     'p <- miaViz::plotRowGraph(se, name=\"graph\", assay.type=\"counts\",\n    show.label=FALSE, layout=\"kk\", edge.type=\"fan\", add.legend=TRUE)',
+  #     fixed = TRUE)
+
+  expect_true(.hideInterface(panel, "ColumnSelectionSource"))
+  expect_false(.multiSelectionResponsive(panel, "column"))
+  expect_true(.multiSelectionResponsive(panel, "row"))
+
+  expect_contains(slotNames(panel), c("detection", "prevalence", "assay.type",
+      "rank", "include.lowest", "show.rank"))
+
+  expect_contains(.definePanelTour(panel)[[1]],
+      c("#PrevalencePlotNA_DataBoxOpen", "#PrevalencePlotNA",
+      "#PrevalencePlotNA_SelectionBoxOpen"))
+
+  expect_s3_class(.create_visual_box_for_prev_plot(panel, tse), "shiny.tag.list")
+
+  expect_null(.renderOutput(panel, tse, output = output, pObjects = pObjects, rObjects = rObjects))
+  expect_s3_class(output$PrevalencePlotNA, "shiny.render.function")
+  expect_s3_class(output$PrevalencePlotNA_INTERNAL_PanelMultiSelectInfo, "shiny.render.function")
+  expect_s3_class(output$PrevalencePlotNA_INTERNAL_PanelSelectLinkInfo, "shiny.render.function")
+
+  # expect_identical(.exportOutput(panel, tse), "PrevalencePlotNA.pdf")
+
+})

tests/testthat/test-RowGraphPlot.R

@@ -0,0 +1,54 @@
+test_that("RowGraphPlot", {
+
+  output <- new.env()
+  pObjects <- new.env()
+  rObjects <- new.env()
+  select_info <- list(single = list(feature = "---", sample = "---"),
+                      multi = list(row = "---", column = "---"))
+
+  data("GlobalPatterns", package = "mia")
+  tse <- GlobalPatterns
+
+  data("row_graph_order", package = "miaViz")
+
+  tse  <- mia::agglomerateByRank(tse, rank = "Order", na.rm = TRUE)
+  metadata(tse)$graph <- row_graph_order
+
+  panel <- RowGraphPlot()
+
+  panel[["layout"]] <- "kk"
+
+  expect_identical(.getEncodedName(panel), "RowGraphPlotNA")
+  expect_identical(.fullName(panel), "Row graph plot")
+  expect_identical(.panelColor(panel), "orange")
+
+  expect_s3_class(.defineInterface(panel, tse, select_info)[[1]][[1]], "shiny.tag.list")
+  expect_length(.defineDataInterface(panel, tse, select_info), 3)
+
+  expect_s3_class(.defineOutput(panel), "shiny.tag.list")
+  expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
+      'p <- miaViz::plotRowGraph(se, name=\"graph\", assay.type=\"counts\",\n    show.label=FALSE, layout=\"kk\", edge.type=\"fan\", add.legend=TRUE)',
+      fixed = TRUE)
+
+  expect_true(.hideInterface(panel, "ColumnSelectionSource"))
+  expect_false(.multiSelectionResponsive(panel, "column"))
+  expect_true(.multiSelectionResponsive(panel, "row"))
+
+  expect_contains(slotNames(panel), c("name", "assay.type", "layout",
+      "show.label", "add.legend", "edge.colour.by", "edge.size.by",
+      "node.colour.by", "node.shape.by", "node.size.by"))
+
+  expect_contains(.definePanelTour(panel)[[1]],
+      c("#RowGraphPlotNA_DataBoxOpen", "#RowGraphPlotNA_VisualBoxOpen",
+      "#RowGraphPlotNA", "#RowGraphPlotNA_SelectionBoxOpen"))
+
+  expect_s3_class(.create_visual_box_for_graph(panel, tse), "shiny.tag.list")
+
+  expect_null(.renderOutput(panel, tse, output = output, pObjects = pObjects, rObjects = rObjects))
+  expect_s3_class(output$RowGraphPlotNA, "shiny.render.function")
+  expect_s3_class(output$RowGraphPlotNA_INTERNAL_PanelMultiSelectInfo, "shiny.render.function")
+  expect_s3_class(output$RowGraphPlotNA_INTERNAL_PanelSelectLinkInfo, "shiny.render.function")
+
+  expect_identical(.exportOutput(panel, tse), "RowGraphPlotNA.pdf")
+
+})

tests/testthat/test-ScreePlot.R

@@ -0,0 +1,50 @@
+test_that("ScreePlot", {
+
+  output <- new.env()
+  pObjects <- new.env()
+  rObjects <- new.env()
+  select_info <- list(single = list(feature = "---", sample = "---"),
+                      multi = list(row = "---", column = "---"))
+
+  data("Tengeler2020", package = "mia")
+  tse <- Tengeler2020
+  panel <- ScreePlot()
+
+  panel[["show.barplot"]] <- FALSE
+  panel[["show.line"]] <- FALSE
+
+  tse <- scater::runPCA(tse, assay.type = "counts", ncomponents = 5)
+
+  expect_identical(.getEncodedName(panel), "ScreePlotNA")
+  expect_identical(.fullName(panel), "Scree plot")
+  expect_identical(.panelColor(panel), "#0066CC")
+
+  expect_s3_class(.defineInterface(panel, tse, select_info)[[1]][[1]], "shiny.tag.list")
+  expect_length(.defineDataInterface(panel, tse, select_info), 5)
+
+  expect_s3_class(.defineOutput(panel), "shiny.tag.list")
+  expect_match(.generateOutput(panel, tse)[["commands"]][["fun"]],
+  "p <- miaViz::plotScree(se, dimred=\"PCA\", show.barplot=FALSE, show.points=TRUE,\n    show.line=FALSE, add.proportion=TRUE, add.cumulative=FALSE,\n    show.names=FALSE, show.labels=FALSE, n=5)",
+  fixed = TRUE)
+
+  # expect_true(.hideInterface(panel, "ColumnSelectionSource"))
+  # expect_false(.multiSelectionResponsive(panel, "column"))
+  # expect_true(.multiSelectionResponsive(panel, "row"))
+
+  expect_contains(slotNames(panel), c("dimred", "show.barplot", "show.points",
+      "show.line", "show.labels", "add.proportion", "add.cumulative", "n",
+      "show.names", "eig.name"))
+
+  expect_contains(.definePanelTour(panel)[[1]],
+      c("#ScreePlotNA_DataBoxOpen"))
+
+  expect_s3_class(.create_visual_box_for_scree_plot(panel, tse), "shiny.tag.list")
+
+  expect_null(.renderOutput(panel, tse, output = output, pObjects = pObjects, rObjects = rObjects))
+  expect_s3_class(output$ScreePlotNA, "shiny.render.function")
+  # expect_s3_class(output$ScreePlotNA_INTERNAL_PanelMultiSelectInfo, "shiny.render.function")
+  # expect_s3_class(output$ScreePlotNA_INTERNAL_PanelSelectLinkInfo, "shiny.render.function")
+
+  expect_identical(.exportOutput(panel, tse), "ScreePlotNA.pdf")
+
+})