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testPlot.R
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testPlot.R
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# Test custom plots
# Setup ------------------------------------------------------------------------
# source(paste0(getwd(), "/inst/tinytest/tinytestSettings.R"))
source("tinytestSettings.R")
using(ttdo)
library(OmicNavigator)
testStudyName <- "ABC"
testStudyObj <- OmicNavigator:::testStudy(name = testStudyName)
plots <- OmicNavigator:::testPlots()
testStudyObj <- addPlots(testStudyObj, plots)
testModelName <- names(testStudyObj[["models"]])[1]
tmplib <- tempfile()
dir.create(tmplib)
libOrig <- .libPaths()
.libPaths(c(tmplib, libOrig))
suppressMessages(installStudy(testStudyObj))
testPkgName <- paste0(OmicNavigator:::getPrefix(), testStudyName)
# Test plots in exported package -----------------------------------------------
pkgDependencies <- utils::packageDescription(
testPkgName,
lib.loc = tmplib,
fields = "Imports"
)
expect_identical_xl(
pkgDependencies,
"data.table, ggplot2, graphics, plotly, rlang, stats"
)
pkgExports <- sort(getNamespaceExports(testPkgName))
plotsAll <- sort(unlist(lapply(plots, names), use.names = FALSE))
expect_identical_xl(
pkgExports,
plotsAll
)
# noMapping (multiModel) -------------------------------------------------------
testStudyObjNoMapping <- testStudyObj
testStudyObjNoMapping[["mapping"]] <- list()
mmodel <- names(testStudyObj[["models"]])[1:2]
mmtestID <- c("test_01", "test_02")
names(mmtestID) <- mmodel
expect_error_xl(
plotStudy(
testStudyObjNoMapping,
modelID = mmodel,
featureID = "feature_0002",
plotID = "multiModel_barplot_sf",
testID = mmtestID
),
"Plot type \"multiModel\" requires mapping object"
)
testStudyObjNoMapping[["mapping"]] <- NULL
expect_error_xl(
plotStudy(
testStudyObjNoMapping,
modelID = mmodel,
featureID = "feature_0002",
plotID = "multiModel_barplot_sf",
testID = mmtestID
),
"Plot type \"multiModel\" requires mapping object"
)
# plotStudy (object) -----------------------------------------------------------
pkgsAttachedPre <- search()
parSettingsPre <- graphics::par(no.readonly = TRUE)
expect_silent_xl(
plotStudy(testStudyObj, modelID = "model_01", featureID = "feature_0001", plotID = "plotBase")
)
expect_silent_xl(
plotStudy(testStudyObj, modelID = "model_02", featureID = "feature_0001", plotID = "plotBase")
)
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_03", featureID = "feature_0001", plotID = "plotBase")
)
#plotly
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_01", featureID = "feature_0001", plotID = "plotPlotly")
)
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_01", featureID = "feature_0001", plotID = "plotGg")
)
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_02", featureID = "feature_0001", plotID = "plotGg")
)
expect_silent_xl(
plotStudy(testStudyObj, modelID = "model_03", featureID = "feature_0001", plotID = "plotGg")
)
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_01", featureID = "feature_0001", plotID = "non-existent"),
"non-existent"
)
expect_error_xl(
plotStudy(testStudyObj, modelID = "model_01", featureID = "non-existent", plotID = "plotBase"),
"non-existent"
)
# plotStudy (package) ----------------------------------------------------------
# Remove plotting functions from current environment. This ensures that the
# calls to plotStudy() below obtain the plotting functions from the package
# namespace.
rm(list = plotsAll)
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001", plotID = "plotBase")
)
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_02", featureID = "feature_0001", plotID = "plotBase")
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_03", featureID = "feature_0001", plotID = "plotBase")
)
#plotly
expect_error_xl(
plotStudy(testStudyName, modelID = "model_04", featureID = "feature_0001", plotID = "plotPlotly")
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001", plotID = "plotGg")
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_02", featureID = "feature_0001", plotID = "plotGg")
)
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_03", featureID = "feature_0001", plotID = "plotGg")
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001", plotID = "non-existent"),
"non-existent"
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "non-existent", plotID = "plotBase"),
"non-existent"
)
pkgsAttachedPost <- search()
expect_identical_xl(
pkgsAttachedPost,
pkgsAttachedPre
)
parSettingsPost <- graphics::par(no.readonly = TRUE)
expect_identical_xl(
parSettingsPost,
parSettingsPre
)
# plotStudy (multiFeature) -----------------------------------------------------
expect_silent_xl(
plotStudy(
testStudyName,
modelID = "model_01",
featureID = c("feature_0026", "feature_0001"),
plotID = "plotMultiFeature"
)
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = "model_01",
featureID = c("feature_0001"),
plotID = "plotMultiFeature"
),
"Received 1 featureID\\(s\\)",
info = "Cannot pass a single featureID to a multiFeature plot"
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = "model_01",
featureID = c("feature_0026", "feature_0001"),
plotID = "plotBase"
),
"Received 2 featureID\\(s\\)",
info = "Cannot pass multiple featureIDs to a singleFeature plot"
)
# plotStudy (multiModel) -------------------------------------------------------
mmodel <- names(testStudyObj[["models"]])[1:2]
mmtestID <- c("test_01", "test_02")
expect_silent_xl(
plotStudy(
testStudyName,
modelID = mmodel,
featureID = c("feature_0002", "feature_0010", "feature_0026"),
plotID = "multiModel_scatterplot",
testID = mmtestID
)
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = mmodel,
featureID = c("feature_0026", "feature_0001", "feature_0002", "feature_0010"),
plotID = "multiModel_scatterplot",
testID = mmtestID[1]
),
"Plot type \"multiModel\" requires testID to be either NULL \\(default\\) or a vector containing at least 2 testIDs"
)
expect_message_xl(
plotStudy(
testStudyName,
modelID = mmodel,
featureID = c("feature_0026", "feature_0001", "feature_0002", "feature_0010"),
plotID = "multiModel_scatterplot",
testID = c("test_01", "test_02")
),
"The provided features list contains at least one feature not present in model"
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = mmodel,
featureID = c("feature_0001"),
plotID = "multiModel_barplot_sf",
testID = c("test_01", "test_02")
),
"The provided features list does not contain any feature present in model"
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = names(testStudyObj[["models"]]),
featureID = "feature_0002",
plotID = "multiModel_barplot_sf",
testID = mmtestID
),
"For multimodel plots modelID and testID are required to be vectors of the same length or testID to be set to NULL"
)
expect_error_xl(
plotStudy(
testStudyName,
modelID = mmodel,
featureID = c("feature_0020006", "feature_0001", "feature_0002"),
plotID = "multiModel_barplot_sf",
testID = mmtestID
),
"Plot type \"singleFeature\" requires 1 featureID"
)
# plotStudy (testID) -----------------------------------------------------------
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001",
plotID = "plotBase", testID = "test_01")
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001",
plotID = "plotBase", testID = "non-existent"),
"non-existent"
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "non-existent",
plotID = "plotBase", testID = "test_01"),
"non-existent"
)
# plotStudy (multitest) --------------------------------------------------------
## check plotStudy calls without checking getPlottingData outputs
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001",
plotID = "plotMultiTestSf", testID = c("test_01", "test_02"))
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "non-existent",
plotID = "plotMultiTestSf", testID = c("test_01", "test_02")),
"non-existent"
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01", featureID = "feature_0001",
plotID = "plotMultiTestSf", testID = "test_01")
)
expect_silent_xl(
plotStudy(testStudyName, modelID = "model_01",
featureID = c("feature_0001", "feature_0002"),
plotID = "plotMultiTestMf", testID = c("test_01", "test_02"))
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01",
featureID = "non-existent",
plotID = "plotMultiTestMf", testID = c("test_01", "test_02"))
)
expect_error_xl(
plotStudy(testStudyName, modelID = "model_01",
featureID = c("feature_0001", "feature_0002"),
plotID = "plotMultiTestMf", testID = "test_01")
)
# getPlottingData (object) -----------------------------------------------------
plottingData <- getPlottingData(
testStudyObj,
modelID = testModelName,
featureID = "feature_0001"
)
assays <- getAssays(testStudyObj, modelID = testModelName)
samples <- getSamples(testStudyObj, modelID = testModelName)
features <- getFeatures(testStudyObj, modelID = testModelName)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
plottingData[["assays"]],
assays["feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_equal_xl(
plottingData[["samples"]],
samples
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
plottingData[["features"]],
features[features[[1]] == "feature_0001", ]
)
# getPlottingData (package) ----------------------------------------------------
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = "feature_0001"
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
plottingData[["assays"]],
assays["feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_equal_xl(
plottingData[["samples"]],
samples
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
plottingData[["features"]],
features[features[[1]] == "feature_0001", ]
)
# getPlottingData (object, multiFeature) ---------------------------------------
plottingData <- getPlottingData(
testStudyObj,
modelID = testModelName,
featureID = c("feature_0001", "feature_0002")
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["assays"]]),
2
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["features"]]),
2
)
# getPlottingData (package, multiFeature) --------------------------------------
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = c("feature_0001", "feature_0002")
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["assays"]]),
2
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["features"]]),
2
)
rm(plottingData)
# getPlottingData (object, multiModel) -----------------------------------------
mmodel <- names(testStudyObj[["models"]])[1:2]
mmtestID <- c("test_01", "test_02")
plottingData <- getPlottingData(
testStudyObj,
modelID = mmodel,
featureID = c("feature_0010", "feature_0020"),
testID = mmtestID
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData)[1:2],
mmodel
)
expect_identical_xl(
names(plottingData[[1]]),
c("assays", "samples", "features", "results")
)
expect_identical_xl(
names(plottingData[[1]][[4]]),
c("test_01")
)
expect_identical_xl(
names(plottingData[[2]]),
c("assays", "samples", "features", "results")
)
expect_identical_xl(
names(plottingData[[2]][[4]]),
c("test_02")
)
expect_true_xl(
inherits(plottingData[[1]][["assays"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[[1]][["assays"]]),
2
)
expect_true_xl(
inherits(plottingData[[1]][["samples"]], "data.frame")
)
expect_true_xl(
inherits(plottingData[[1]][["features"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[[1]][["features"]]),
2
)
expect_true_xl(
inherits(plottingData[[1]][["results"]], "list")
)
rm(plottingData)
# getPlottingData (package, multiModel) -----------------------------------------
mmodel <- names(testStudyObj[["models"]])[1:2]
mmtestID <- c("test_01", "test_02")
names(mmtestID) <- mmodel
plottingData <- getPlottingData(
testStudyName,
modelID = mmodel,
featureID = c("feature_0010", "feature_0020"),
testID = mmtestID
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData)[1:2],
mmodel
)
expect_identical_xl(
names(plottingData[[1]]),
c("assays", "samples", "features", "results")
)
expect_identical_xl(
names(plottingData[[1]][[4]]),
c("test_01")
)
expect_identical_xl(
names(plottingData[[2]]),
c("assays", "samples", "features", "results")
)
expect_identical_xl(
names(plottingData[[2]][[4]]),
c("test_02")
)
expect_true_xl(
inherits(plottingData[[1]][["assays"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[[1]][["assays"]]),
2
)
expect_true_xl(
inherits(plottingData[[1]][["samples"]], "data.frame")
)
expect_true_xl(
inherits(plottingData[[1]][["features"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[[1]][["features"]]),
2
)
expect_true_xl(
inherits(plottingData[[1]][["results"]], "list")
)
rm(plottingData)
# getPlottingData (edge cases) -------------------------------------------------
# Duplicate featureIDs should be deduplicated
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = c("feature_0001", "feature_0001")
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["assays"]]),
1
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
nrow(plottingData[["features"]]),
1
)
# Ensure that getPlottingData() sorts the 3 data frames to match
needsSorting <- createStudy("needsSorting")
needsSortingSamples <- data.frame(sampleID = c("three", "one", "two"),
sampleVar = letters[1:3],
stringsAsFactors = FALSE)
needsSorting <- addSamples(needsSorting, list(default = needsSortingSamples))
needsSortingFeatures <- data.frame(featureID = c("f4", "f5", "f1", "f3", "f2"),
featureVar = letters[1:5],
stringsAsFactors = FALSE)
needsSorting <- addFeatures(needsSorting, list(default = needsSortingFeatures))
needsSortingAssays <- matrix(rnorm(5 * 3), nrow = 5, ncol = 3)
needsSortingAssays <- as.data.frame(needsSortingAssays)
row.names(needsSortingAssays) <- paste0("f", 1:5)
names(needsSortingAssays) <- c("one", "two", "three")
needsSorting <- addAssays(needsSorting, list(main = needsSortingAssays))
sortedPlottingData <- getPlottingData(
needsSorting,
modelID = "main",
featureID = c("f2", "f1", "f3")
)
expect_identical_xl(
sortedPlottingData[["samples"]][[1]],
colnames(sortedPlottingData[["assays"]]),
info = "Samples metadata rows should match assays columns"
)
expect_identical_xl(
sortedPlottingData[["features"]][[1]],
c("f2", "f1", "f3"),
info = "Features metadata for plotting are sorted according to input featureIDs"
)
expect_identical_xl(
rownames(sortedPlottingData[["assays"]]),
c("f2", "f1", "f3"),
info = "Assays rows for plotting are sorted according to input featureIDs"
)
# getPlottingData() should send warning if featureID or sampleID is missing
# metadata.
needsSortingAssaysExtra <- cbind(needsSortingAssays, four = rnorm(5))
needsSortingAssaysExtra <- rbind(needsSortingAssaysExtra, f6 = rnorm(4))
needsSorting <- addAssays(needsSorting, list(extra = needsSortingAssaysExtra))
expect_warning(
getPlottingData(
needsSorting,
modelID = "extra",
featureID = c("f2", "f1", "f3")
),
"Not all of the sampleIDs have metadata",
info = "Warning when assays has a column that is missing from the samples table"
)
expect_warning(
getPlottingData(
needsSorting,
modelID = "extra",
featureID = c("f2", "f1", "f3", "f6")
),
"Not all of the featureIDs have metadata",
info = "Warning when assays has a row that is missing from the features table"
)
# getPlottingData() can work even if the only data returned is "results"
testStudyObjMinimal <- OmicNavigator:::testStudyMinimal()
plottingDataMinimal <- getPlottingData(
testStudyObjMinimal,
modelID = testModelName,
featureID = "feature_0001",
testID = "test_01"
)
expect_identical_xl(
plottingDataMinimal[["assays"]],
list()
)
expect_identical_xl(
plottingDataMinimal[["samples"]],
list()
)
expect_identical_xl(
plottingDataMinimal[["features"]],
list()
)
expect_true_xl(
inherits(plottingDataMinimal[["results"]], "data.frame")
)
expect_identical_xl(
plottingDataMinimal[["results"]][[1]],
"feature_0001"
)
# getPlottingData (object, testID) ---------------------------------------------
plottingData <- getPlottingData(
testStudyObj,
modelID = testModelName,
featureID = "feature_0001",
testID = "test_01"
)
assays <- getAssays(testStudyObj, modelID = testModelName)
samples <- getSamples(testStudyObj, modelID = testModelName)
features <- getFeatures(testStudyObj, modelID = testModelName)
results <- getResults(testStudyObj, modelID = testModelName, testID = "test_01")
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features", "results")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
plottingData[["assays"]],
assays["feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_equal_xl(
plottingData[["samples"]],
samples
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
plottingData[["features"]],
features[features[[1]] == "feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["results"]], "data.frame")
)
expect_equal_xl(
plottingData[["results"]],
results[results[[1]] == "feature_0001", ]
)
# getPlottingData (package, testID) --------------------------------------------
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = "feature_0001",
testID = "test_01"
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features", "results")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
plottingData[["assays"]],
assays["feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_equal_xl(
plottingData[["samples"]],
samples
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
plottingData[["features"]],
features[features[[1]] == "feature_0001", ]
)
expect_true_xl(
inherits(plottingData[["results"]], "data.frame")
)
expect_equal_xl(
plottingData[["results"]],
results[results[[1]] == "feature_0001", ]
)
# getPlottingData (package, multitest) -----------------------------------------
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = c("feature_0001", "feature_0002"),
testID = c("test_01", "test_02")
)
expect_true_xl(
inherits(plottingData, "list")
)
expect_identical_xl(
names(plottingData),
c("assays", "samples", "features", "results")
)
expect_true_xl(
inherits(plottingData[["assays"]], "data.frame")
)
expect_equal_xl(
plottingData[["assays"]],
assays[c("feature_0001", "feature_0002"), ]
)
expect_true_xl(
inherits(plottingData[["samples"]], "data.frame")
)
expect_equal_xl(
plottingData[["samples"]],
samples
)
expect_true_xl(
inherits(plottingData[["features"]], "data.frame")
)
expect_equal_xl(
plottingData[["features"]],
features[features[[1]] == c("feature_0001", "feature_0002"), ]
)
expect_true_xl(
inherits(plottingData[["results"]], "list")
)
result_test01 <- testStudyObj$results[[testModelName]]$test_01
result_test01 <- result_test01[order(result_test01$customID),]
expect_equal_xl(
plottingData[["results"]][["test_01"]],
result_test01[result_test01$customID %in% c("feature_0001", "feature_0002"),]
)
result_test02 <- testStudyObj$results[[testModelName]]$test_02
result_test02 <- result_test02[order(result_test02$customID),]
expect_equal_xl(
plottingData[["results"]][["test_02"]],
result_test02[result_test02$customID %in% c("feature_0001", "feature_0002"),]
)
# getPlottingData (package, multiFeature, testID) ------------------------------
plottingData <- getPlottingData(
testStudyName,
modelID = testModelName,
featureID = c("feature_0006", "feature_0002"),
testID = "test_01"
)
expect_identical_xl(
plottingData[["results"]][[1]],
c("feature_0006", "feature_0002")
)
# Plotly Plots -----------------------------------------------------------------
json <- plotStudy(testStudyName, modelID = "model_03", featureID = "feature_0001", plotID = "plotPlotly")
expect_true_xl(
inherits(json, "json")
)
# Catch plots of plotType "plotly" that don't correctly return a plotly plot
notPlotlyFunc <- function(x) graphics::plot(1:10)
notPlotlyFuncList <- list(
default = list(
notPlotlyFunc = list(
displayName = "notPlotly",
plotType = "plotly",
packages = "plotly"
)
)
)
testStudyNotPloty <- addPlots(testStudyObj, notPlotlyFuncList)
expect_error(
plotStudy(testStudyNotPloty, modelID = "model_01", featureID = "feature_0001", plotID = "notPlotlyFunc"),
"The plotID \"notPlotlyFunc\" has plotType \"plotly\" but did not return an object with class \"plotly\"",
info = "Detect invalid plotly functions"
)
# Teardown ---------------------------------------------------------------------
unloadNamespace(testPkgName)
unlink(tmplib, recursive = TRUE, force = TRUE)
.libPaths(libOrig)