recoup (version 1.0.2)

recoupPlot: 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.

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)