recoupPlot: Plot list objects returned by recoup

In pmoulos/recoup: An R package for the creation of complex genomic profile plots

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(vapply(recoupObj,
        function(x) return(x$data$id), character(1)), 
        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=0.1
)

# Plot coverage profiles
recoupPlot(test.tss)

pmoulos/recoup documentation built on March 14, 2024, 5:21 p.m.