MAPlot-class: The MAPlot class

Description Slot overview Constructor Supported methods Author(s) See Also Examples

Description

The MAPlot is a RowDataPlot subclass that is dedicated to creating a MA plot. It retrieves the log-fold change and average abundance and creates a row-based plot where each point represents a feature. Users are expected to load relevant statistics into the rowData of a SummarizedExperiment.

Slot overview

The following slots control the thresholds used in the visualization:

The following slots control the choice of columns in the user interface:

In addition, this class inherits all slots from its parent RowDataPlot, RowDotPlot, DotPlot and Panel classes.

Constructor

MAPlot(...) creates an instance of a MAPlot class, where any slot and its value can be passed to ... as a named argument.

Initial values for PValuePattern, AveAbPattern and LogFCPattern are set to the outputs of getPValuePattern, getAveAbPattern and getLogFCPattern, respectively. These parameters are considered to be global constants and cannot be changed inside the running iSEE application. Similarly, it is not possible for multiple MAPlots in the same application to have different values for these slots; within the app, all values are set to those of the first encountered MAPlot to ensure consistency.

Supported methods

In the following code snippets, x is an instance of a RowDataPlot class. Refer to the documentation for each method for more details on the remaining arguments.

For setting up data values:

For defining the interface:

For monitoring reactive expressions:

For creating the plot:

For documentation:

Author(s)

Aaron Lun

See Also

RowDataPlot, for the base class.

Examples

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# Making up some results:
se <- SummarizedExperiment(matrix(rnorm(10000), 1000, 10))
rownames(se) <- paste0("GENE_", seq_len(nrow(se)))
rowData(se)$PValue <- runif(nrow(se))
rowData(se)$LogFC <- rnorm(nrow(se))
rowData(se)$AveExpr <- rnorm(nrow(se))

if (interactive()) {
    iSEE(se, initial=list(MAPlot()))
}

iSEEu documentation built on Nov. 8, 2020, 8:12 p.m.