simpleGetSet {recoup} | R Documentation

## Get and set some reusable objects from a recoup object

### Description

The `getr` and `setr` functions are used to get several reusable/changeable objects of `recoup` or replcace them (e.g. when the user wishes to change some `ggplot` or `ComplexHeatmap` parameters manually in a plot, or change the heatmap profile ordering mode).

### Usage

        getr(obj, key = c("design", "profile", "heatmap",
            "correlation", "orderBy", "kmParams", "plotParams"))
        setr(obj, key, value = NULL)

### Arguments

`obj` | a list object created from `recoup`.
`key` | one of `"design"`, `"profile"`, `"heatmap"`, `"correlation"`, `orderBy`, `kmParams`, `plotParams`. For `"profile"`, `"heatmap"`, the respective plots are retrieved or changed according to which function is called. For `setr` it can (and preferably) be a named list of arguments to be changed in the `recoup` list object. The list names are the same as above. For the rest, see the main `recoup` man page.
`value` | a valid `ggplot` or `HeatmapList` object created from `recoupProfile` or `recoupHeatmap` `recoupCorrelation` when changing plots. Values for all other types are also checked for validity.

### Value

For `getr`, the object asked to be retrieved. For `setr`, the `obj` with the respective slots filled or replaced with `value`.

### Author(s)

Panagiotis Moulos

### Examples

    # Load some data
    data("recoup_test_data",package="recoup")

    # Calculate coverages
    test.tss <- recoup(
        test.input,
        design=NULL,
        region="tss",
        type="chipseq",
        genome=test.genome,
        flank=c(2000,2000),
        selector=NULL,
        plotParams=list(plot=FALSE,profile=TRUE,
            heatmap=TRUE,device="x11"),
        rc=0.1
    )

    # Plot coverage profiles

    # Get the curve profile plot
    pp <- getr(test.tss,"profile")

    # Change some ggplot parameter
    pp <- pp +
        theme(axis.title.x=element_text(size=14))

    # Store the new plot
    test.tss <- setr(test.tss,"profile",pp)
    ## or even better
    # test.tss <- setr(test.tss,list(profile=pp))

[Package recoup version 1.20.1 Index]