getPlottingData {OmicNavigator}

Get plotting data

Description

This function creates the input data that plotStudy passes to custom plotting functions added with addPlots. You can use it directly when you are interactively creating your custom plotting functions. Note that for multiModel plots testID is required to be a named vector, with each testID named after the related modelID.

Usage

getPlottingData(study, modelID, featureID, testID = NULL, libraries = NULL)

Arguments

study

An OmicNavigator study. Either an object of class onStudy, or the name of an installed study package.

modelID

Filter by modelID

featureID

Filter by featureID

testID

Filter by testID

libraries

The directories to search for installed study packages. If left as NULL (the default), then installed.packages will use the result of .libPaths.

Value

Returns a list of 4 data frames:

assays

A data frame that contains the assay measurements, filtered to only include the row(s) corresponding to the input featureID(s) (see getAssays). If multiple featureIDs are requested, the rows are reordered to match the order of this input. The column order is unchanged.

samples

A data frame that contains the sample metadata for the given modelID (see getSamples). The rows are reordered to match the columns of the assays data frame.

features

A data frame that contains the feature metadata, filtered to only include the row(s) corresponding to the input featureID(s) (see getFeatures). If multiple featureIDs are requested, the rows are reordered to match the order of this input (and thus match the order of the assays data frame).

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. If multiple testIDs are provided, they are stored in a list object.

The data frame results is only returned if you pass a testID. By default the app will always pass the currently selected testID. To make results a list of data frames (one for each testID for the currently selected modelID), set the plotType to be "multiTest" when adding the plot with addPlots. For "multiModel" plots, testID and modelID should be vectors of same length, where the index position indicate which test in testID relate to which model in modelID.

See Also

addPlots, plotStudy