tests/testthat/apps/sce_app/tests/shinytest/gating_1.R

In BodenmillerGroup/SingleCellMapper: Visualization of highly multiplexed imaging data in R

app <- ShinyDriver$new("../../", loadTimeout = 100000, seed = 1234)
app$snapshotInit("gating_1")

brush1 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 12,
               ymax = 34,
               mapping = list(x = "sample",
                              y = "CD99"),
               direction = "xy",
               brushId = "plot_brush1",
               outputId = "scatter1")

brush2 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 0,
               ymax = 3,
               mapping = list(x = "sample",
                              y = "CD8a"),
               direction = "xy",
               brushId = "plot_brush2",
               outputId = "scatter2")

brush3 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 10,
               ymax = 20,
               mapping = list(x = "sample",
                              y = "CDH"),
               direction = "xy",
               brushId = "plot_brush3",
               outputId = "scatter3")


app$setInputs(plotCount = 3)
Sys.sleep(0.5)
app$snapshot()
app$setInputs(Marker_1 = "CD99")
app$snapshot()
app$setInputs(plot_brush1 = brush1, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_3 = "CD8a")
app$snapshot()
app$setInputs(plot_brush2 = brush2, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_5 = "CDH")
app$snapshot()
app$setInputs(plot_brush3 = brush3, allowInputNoBinding_ = TRUE)
app$snapshot()

app$setInputs(plotCount = 1)
app$setInputs(plotCount = 3)

app$snapshot()

brush1 <- list(xmin = 5,
               xmax = 34,
               ymin = 10,
               ymax = 60,
               mapping = list(x = "CD99",
                              y = "H3"),
               direction = "xy",
               brushId = "plot_brush1",
               outputId = "scatter1")

brush2 <- list(xmin = 5,
               xmax = 30,
               ymin = 0,
               ymax = 40,
               mapping = list(x = "PIN",
                              y = "CDH"),
               direction = "xy",
               brushId = "plot_brush2",
               outputId = "scatter2")

brush3 <- list(xmin = 0,
               xmax = 20,
               ymin = 10,
               ymax = 40,
               mapping = list(x = "CD8a",
                              y = "CD99"),
               direction = "xy",
               brushId = "plot_brush3",
               outputId = "scatter3")

app$setInputs(Marker_1 = "CD99")
app$setInputs(Marker_2 = "H3")
app$snapshot()
app$setInputs(plot_brush1 = brush1, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_3 = "PIN")
app$setInputs(Marker_4 = "CDH")
app$snapshot()
app$setInputs(plot_brush2 = brush2, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_5 = "CD8a")
app$setInputs(Marker_6 = "CD99")
app$snapshot()
app$setInputs(plot_brush3 = brush3, allowInputNoBinding_ = TRUE)
app$snapshot()

app$setInputs(plotCount = 1)
app$setInputs(plotCount = 3)
app$setInputs(assay = "exprs")

app$snapshot()

brush1 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 3,
               ymax = 4.5,
               mapping = list(x = "sample",
                              y = "CD99"),
               direction = "xy",
               brushId = "plot_brush1",
               outputId = "scatter1")

brush2 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 0,
               ymax = 2,
               mapping = list(x = "sample",
                              y = "CD8a"),
               direction = "xy",
               brushId = "plot_brush2",
               outputId = "scatter2")

brush3 <- list(xmin = 0.5,
               xmax = 1.5,
               ymin = 3,
               ymax = 4,
               mapping = list(x = "sample",
                              y = "CDH"),
               direction = "xy",
               brushId = "plot_brush3",
               outputId = "scatter3")

app$snapshot()
app$setInputs(Marker_1 = "CD99")
app$snapshot()
app$setInputs(plot_brush1 = brush1, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_3 = "CD8a")
app$snapshot()
app$setInputs(plot_brush2 = brush2, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_5 = "CDH")
app$snapshot()
app$setInputs(plot_brush3 = brush3, allowInputNoBinding_ = TRUE)
app$snapshot()

app$setInputs(plotCount = 1)
app$setInputs(plotCount = 3)

app$snapshot()

brush1 <- list(xmin = 1,
               xmax = 4,
               ymin = 2,
               ymax = 6,
               mapping = list(x = "CD99",
                              y = "H3"),
               direction = "xy",
               brushId = "plot_brush1",
               outputId = "scatter1")

brush2 <- list(xmin = 1,
               xmax = 4,
               ymin = 0,
               ymax = 4,
               mapping = list(x = "PIN",
                              y = "CDH"),
               direction = "xy",
               brushId = "plot_brush2",
               outputId = "scatter2")

brush3 <- list(xmin = 0,
               xmax = 3,
               ymin = 1,
               ymax = 4,
               mapping = list(x = "CD8a",
                              y = "CD99"),
               direction = "xy",
               brushId = "plot_brush3",
               outputId = "scatter3")

app$setInputs(Marker_1 = "CD99")
app$setInputs(Marker_2 = "H3")
app$snapshot()
app$setInputs(plot_brush1 = brush1, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_3 = "PIN")
app$setInputs(Marker_4 = "CDH")
app$snapshot()
app$setInputs(plot_brush2 = brush2, allowInputNoBinding_ = TRUE)
app$snapshot()
app$setInputs(Marker_5 = "CD8a")
app$setInputs(Marker_6 = "CD99")
app$snapshot()
app$setInputs(plot_brush3 = brush3, allowInputNoBinding_ = TRUE)
app$snapshot()


p <- app$.__enclos_env__$private$shinyProcess
p$interrupt()
p$wait()