LogFCLogFCPlot-class {iSEEu}R Documentation

The LogFCLogFCPlot class

Description

The LogFCLogFCPlot is a RowDataPlot subclass that is dedicated to creating a scatter plot of two log-fold changes. Each axis contains the log-fold change for a differential expression analysis and each point represents a feature.

Slot overview

The following slots control the thresholds used in the visualization:

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

Constructor

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

Users are expected to load relevant statistics into the rowData of a SummarizedExperiment. There should be two columns for the p-values from each comparison - and another two for the corresponding log-fold changes - for each gene/row, see Examples. The expected column names (and how to tune them) are listed at ?"registerPValueFields".

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

# Making up some results:
se <- SummarizedExperiment(matrix(rnorm(10000), 1000, 10))
rownames(se) <- paste0("GENE_", seq_len(nrow(se)))
rowData(se)$PValue1 <- runif(nrow(se))
rowData(se)$LogFC1 <- rnorm(nrow(se))
rowData(se)$PValue2 <- runif(nrow(se))
rowData(se)$LogFC2 <- rnorm(nrow(se))

if (interactive()) {
    iSEE(se, initial=list(LogFCLogFCPlot(XAxisRowData="LogFC1", YAxis="LogFC2",
        XPValueField="PValue1", YPValueField="PValue2")))
}


[Package iSEEu version 1.4.0 Index]