plotStudy and getPlottingData functions accept parameter testID.

R/plots.R

@@ -10,11 +10,12 @@
 #' @seealso \code{\link{addPlots}}, \code{\link{getPlottingData}}
 #'
 #' @export
-plotStudy <- function(study, modelID, featureID, plotID, libraries = NULL) {
+plotStudy <- function(study, modelID, featureID, plotID, testID = NULL, libraries = NULL) {
   stopifnot(
     is.character(modelID),
     is.character(featureID),
     is.character(plotID),
+    is.null(testID) || is.character(testID),
     is.null(libraries) || is.character(libraries)
   )
 
@@ -49,7 +50,7 @@ plotStudy <- function(study, modelID, featureID, plotID, libraries = NULL) {
     )
   }
 
-  plottingData <- getPlottingData(study, modelID, featureID,
+  plottingData <- getPlottingData(study, modelID, featureID, testID = testID,
                                   libraries = libraries)
 
   # Setup for the plot and ensure everything is properly reset after the
@@ -136,13 +137,19 @@ resetSearch <- function(pkgNamespaces) {
 #' rows are reordered to match the order of this input (and thus match the order
 #' of the assays data frame).}
 #'
+#' \item{\code{results}}{A data frame that contains the test results,
+#' filtered to only include the row(s) corresponding to the input featureID(s).
+#' If multiple featureIDs are requested, the rows are reordered to match the
+#' order of this input. The column order is unchanged.}
+#'
 #' @seealso \code{\link{addPlots}}, \code{\link{plotStudy}}
 #'
 #' @export
-getPlottingData <- function(study, modelID, featureID, libraries = NULL) {
+getPlottingData <- function(study, modelID, featureID, testID = NULL, libraries = NULL) {
   stopifnot(
     is.character(modelID),
     is.character(featureID),
+    is.null(testID) || is.character(testID),
     is.null(libraries) || is.character(libraries)
   )
   # Deduplicate the featureIDs
@@ -186,10 +193,26 @@ getPlottingData <- function(study, modelID, featureID, libraries = NULL) {
     row.names(featuresPlotting) <- NULL # reset row numbers after filtering
   }
 
+  if (!isEmpty(testID)) {
+    results <- getResults(study, modelID = modelID, testID = testID, quiet = TRUE,
+                          libraries = libraries)
+    if (isEmpty(results)) {
+      stop(sprintf("The test result (testID) \"%s\" is not available for modelID \"%s\" ", testID, modelID))
+    }
+    featureIDAvailable_results <- featureID %in% results[,1]
+    if (any(!featureIDAvailable_results)) {
+      stop(sprintf("The feature \"%s\" is not available for testID \"%s\"",
+                   featureID[!featureIDAvailable][1], testID))
+    }
+    resultsPlotting <- results[match(featureID, results[,1], nomatch = 0), , drop = FALSE]
+  }
+
   plottingData <- list(
     assays = assaysPlotting,
     samples = samplesPlotting,
     features = featuresPlotting
   )
+  if (!isEmpty(testID))  plottingData <- c(plottingData, list(results = resultsPlotting))
+
   return(plottingData)
 }

inst/tinytest/testPlot.R

@@ -381,6 +381,71 @@ expect_warning(
   info = "Warning when assays has a row that is missing from the features table"
 )
 
+
+# getPlottingData (testID) -----------------------------------------------------
+
+plottingData <- getPlottingData(
+  testStudyObj,
+  modelID = testModelName,
+  featureID = "feature_0001",
+  testID = "test_01"
+)
+
+samples <- getSamples(testStudyObj, modelID = testModelName)
+assays <- getAssays(testStudyObj, modelID = testModelName)
+results <- getResults(testStudyObj, modelID = testModelName, testID = "test_01")
+
+expect_true_xl(
+  inherits(plottingData, "list")
+)
+
+expect_true_xl(
+  inherits(plottingData[["assays"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["samples"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["features"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["results"]], "data.frame")
+)
+
+plottingData <- getPlottingData(
+  testStudyName,
+  modelID = testModelName,
+  featureID = "feature_0001",
+  testID = "test_01"
+)
+
+samples <- getSamples(testStudyName, modelID = testModelName)
+assays <- getAssays(testStudyName, modelID = testModelName)
+results <- getResults(testStudyName, modelID = testModelName, testID = "test_01")
+
+expect_true_xl(
+  inherits(plottingData, "list")
+)
+
+expect_true_xl(
+  inherits(plottingData[["assays"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["samples"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["features"]], "data.frame")
+)
+
+expect_true_xl(
+  inherits(plottingData[["results"]], "data.frame")
+)
+
 # Teardown ---------------------------------------------------------------------
 
 unloadNamespace(testPkgName)

vignettes/OmicNavigatorAPI.Rnw

@@ -210,7 +210,7 @@ toJSON(linkFeatures[1:4], pretty = TRUE)
 \label{sec:custom-plots}
 
 Display the custom plots provided by the user with \texttt{plotStudy()}. Provided a
-study, model, feature, and plot, \texttt{plotStudy()} generates the custom plot.
+study, model, feature, test and plot, \texttt{plotStudy()} generates the custom plot.
 
 The featureID is obtained from the first column returned by
 \texttt{getResultsTable()} (Section \ref{sec:results-table}). The remaining arguments
@@ -222,7 +222,8 @@ plotStudy(
   study = "ABC",
   modelID = "model_01",
   featureID = "feature_0001",
-  plotID = "plotBase"
+  plotID = "plotBase",
+  testID = "test_01"
 )
 @
 
@@ -231,7 +232,8 @@ plotStudy(
   study = "ABC",
   modelID = "model_03",
   featureID = "feature_0001",
-  plotID = "plotGg"
+  plotID = "plotGg",
+  testID = "test_01"
 )
 @
 
@@ -245,7 +247,8 @@ plotStudy(
   study = "ABC",
   modelID = "model_01",
   featureID = c("feature_0001", "feature_0002"),
-  plotID = "plotMultiFeature"
+  plotID = "plotMultiFeature",
+  testID = "test_01"
 )
 @
 

vignettes/OmicNavigatorUsersGuide.Rnw

@@ -1041,6 +1041,10 @@ plotStudy(study, modelID = "main", featureID = c("21390", "19216"),
           plotID = "plotPca")
 @
 
+Optionally, data related to test results can be plotted by providing a valid
+testID to the plotStudy call. For instance, for modelID = "main" one could call
+plotStudy with testID = "basal.vs.lp" to be able to plot its test results.
+
 To make the custom plotting functions available in the app, re-install the study
 package with \texttt{installStudy()}.