plotStudy() invokes a custom plotting function saved within an
OmicNavigator study. This function is called by the app using the
study-model-test selection, feature selections, and plotting function
metadata (see addPlots()) to define arguments.
plotStudy(study, modelID, featureID, plotID, testID = NULL, libraries = NULL)This function is called for the side effect of creating a plot. It
invisibly returns the result from the custom plotting function specified by
plotID. Previously it invisibly returned the study object. It's unlikely
you relied on this behavior. For a ggplot2 plot, the return value will be
the plotting object with class "ggplot". For a plotly plot, the return
value will be the json schema used for plotting with class “json”.
An OmicNavigator study. Either an object of class onStudy,
or the name of an installed study package.
Filter by modelID
Filter by featureID
Filter by plotID
Filter by testID
Character vector of library directories to search for study
packages. If NULL, uses .libPaths.
The arguments study, modelID, featureID, and
testID are passed to the function getPlottingData(). The list returned
by getPlottingData() is passed as the first argument to a custom plotting
function. Some custom plotTypes (see addPlots()) require care when
being invoked and attention should be paid to how a custom plot will be
rendered by the app. Custom plots with plotType = c(‘multiModel’, ‘singleTest’) accept a modelID vector of length n and a vector of
testIDs length n, where n is the number of models. Custom plots with
plotType = c(‘multiModel’, ‘multiTest’) accept modelID and testID
vectors of length m, where m is the total number of tests considered across
all models (note testIDs are often repeated across models). Note that the
index positions of these two vectors should correspond. That is, testID
position 1 should be found in the model specified by modelID position 1,
etc.
The app will invoke custom plotting functions via plotStudy() using the
current menu selections and plot metadata (see addPlots()). Plots with
plotType = ‘multiTest’ will be invoked with all testIDs found within
the currently selected model. Plots with plotType = c(‘multiModel’,‘singleTest’) will be invoked with all modelIDs within
the study (unless the plot has specified a list of models via models) and
the currently selected testID (an error will result if the currently
selected testID is not present in all relevant models for the plot).
Plots with plotType = c(‘multiModel’, ‘multiTest’) will be invoked with
all modelIDs within the study (unless the plot has specified a list of
models via models) and all identical testIDs across models (if there
are no matching testIDs across models an error will result).
addPlots, getPlottingData