plotGenotypesPerCluster: Visualize average counts/enrichment based on strong and weak...

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

Description

The function plotGenotypesPerCluster plots average clusters per genotype based on the clustering results of the strong an weak genotype analysis (see plotAndCalculateWeakAndStrongGenotype), which has to be executed before.

Usage

plotGenotypesPerCluster(SNPhood.o, printBinLabels = TRUE, fileToPlot = NULL,
  printPlot = TRUE, returnOnlyPlotNotObject = FALSE, verbose = FALSE)

Arguments

SNPhood.o	Object of class SNPhood
printBinLabels	Logical(1). Default TRUE. Should the bin labels be printed? If multiple clusters are plotted simultaenously, bin labels might overlap, in which case printBinLabels can be set to FALSE.
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.
printPlot	Logical(1). Default TRUE. Should the plots be printed? Only relevant if fileToPlot is set to NULL; otherwise, the plots are always printed to the output file.
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

plotAndCalculateWeakAndStrongGenotype

Examples

data(SNPhood.o, package="SNPhood")
SNPhood_merged.o = mergeReadGroups(SNPhood.o)
SNPhood_merged.o = plotAndCalculateWeakAndStrongGenotype(SNPhood_merged.o)
plot = plotGenotypesPerCluster(SNPhood_merged.o, printPlot = FALSE)

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