plotClusterAverage: Visualize average enrichment per cluster

In SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

Description

plotClusterAverage visualizes the average reads per cluster. Note that the function plotAndClusterMatrix has to be executed before plotClusterAverage is called for the same read group and dataset

Usage

plotClusterAverage(SNPhood.o, readGroup, dataset, fileToPlot = NULL,
  returnOnlyPlotNotObject = FALSE, verbose = FALSE)

Arguments

SNPhood.o	Object of class SNPhood
readGroup	Character(1). Default NULL. Read group that should be plotted, specified by its name as obtained by the function annotationReadGroups). If only one read group is defined in the object, this may also be NULL for user conveniance.
dataset	Numeric(1) or Character(1). Single dataset that should be used for plotting, either specified as integer (such as 1, value must be between 1 and the total number of datasets as defined in the object) or its annotation (name must appear in the dataset names as obtained via the function annotationDatasets).
fileToPlot	Character(1) or NULL. Default NULL. Filename of the PDF file for the output plots. If set to NULL, plots will be plotted to the currently active device.
returnOnlyPlotNotObject	Logical(1). Default FALSE. If set to TRUE, only the plots are returned but not the actual object. Otherwise, for consistancy among the various visualization functions, the SNPhood object is always returned, while the plots are either written to a PDF file as specified by the parameter fileToPlot and/or to the currently active graphics device (i.e., the console usually)
verbose	Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

the generated ggplot2 plot(s) as list for further processing. May contain multiple plots, depending on the function. The plot(s) can then be plotted individually or modified arbitrarily as the user wants. For example, if multiple plots are returned and the plots have been saved in a variable called plots.l, simply type plots.l[[1]] to view the first plot.

See Also

plotAndClusterMatrix

Examples

data(SNPhood.o, package="SNPhood")
plot = plotClusterAverage(SNPhood.o, readGroup = "paternal", dataset = 1)

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.