plotStudy: Invoke a custom plotting function
| plotStudy | R Documentation |
Invoke a custom plotting function
Description
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.
Usage
plotStudy(study, modelID, featureID, plotID, testID = NULL, libraries = NULL)
Arguments
study |
An OmicNavigator study. Either an object of class |
modelID |
Filter by modelID |
featureID |
Filter by featureID |
plotID |
Filter by plotID |
testID |
Filter by testID |
libraries |
The directories to search for installed study packages. If
left as |
Details
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).
Value
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”.
See Also
addPlots, getPlottingData
