recoupPlot {recoup} | R Documentation

## Plot list objects returned by recoup

### Description

This function takes as input argument an output object from `recoup` and plots the `ggplot2` and `ComplexHeatmap` objects stored there.

### Usage

        recoupPlot(recoupObj, what = c("profile", "heatmap",
            "correlation"), device = c("x11", "png", "jpg", "tiff",
            "bmp", "pdf", "ps"), outputDir = ".",
            outputBase = paste(sapply(recoupObj, function(x)
                return(x$data$id)), sep = "_"), mainh = 1, ...)

### Arguments

`recoupObj` | a list object created from `recoup`.
`what` | one or more of `"profile"`, `"heatmap"` or `"correlation"`. See the `plotParams` in the main `recoup` function. A minimum valid version is provided for default plotting.
`device` | a valid R graphics device. See the `plotParams` in the main `recoup` function.
`outputDir` | a valid directory when device is not `"x11"`. See the `plotParams` in the main `recoup` function.
`outputBase` | a valid file name to be used as basis when device is not `"x11"`. See the `plotParams` in the main `recoup` function. Defaults to a concatenation of sample ids.
`mainh` | the reference heatmap for ordering operations. Normally, calculated in `recoup`. See also the `draw` function in the `ComplexHeatmap` package. Deafults to the first heatmap.
`...` | further parameters passed either to `ggsave` or the base graphics devices of R.

### Value

This function does not returns anything, just plots the `recoup` plots.

### 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=0.5
    )

    # Plot coverage profiles
    recoupPlot(test.tss)

[Package recoup version 1.12.0 Index]