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plotStudy and getPlottingData functions accept parameter testID. #4

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merged 7 commits into from
Aug 18, 2021
Merged

plotStudy and getPlottingData functions accept parameter testID. #4

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c0f3213
- plotStudy and getPlottingData functions accept parameter testID.
Aug 6, 2021
0a3cb3a
Update R/plots.R
curadomr Aug 11, 2021
aac2d27
Update R/plots.R
curadomr Aug 11, 2021
2efc602
Update R/plots.R
curadomr Aug 11, 2021
212021c
Updating documentation on PlotStudy and getPlottingData
Aug 11, 2021
6838a22
Adding unit testing : getPlottingData (testID)
Aug 17, 2021
09fa081
Updating vignettes on testID for plotting functions
Aug 17, 2021
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24 changes: 21 additions & 3 deletions R/plots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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.character(testID),
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is.null(libraries) || is.character(libraries)
)

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -139,10 +140,11 @@ resetSearch <- function(pkgNamespaces) {
#' @seealso \code{\link{addPlots}}, \code{\link{plotStudy}}
#'
#' @export
getPlottingData <- function(study, modelID, featureID, libraries = NULL) {
getPlottingData <- function(study, modelID, featureID, testID, libraries = NULL) {
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stopifnot(
is.character(modelID),
is.character(featureID),
# is.character(testID),
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is.null(libraries) || is.character(libraries)
)
# Deduplicate the featureIDs
Expand Down Expand Up @@ -186,10 +188,26 @@ 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)
}