plotGenotypesPerSNP: Plot genotype frequencies of regions across datasets.

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

Description

Creates bar plots for the distribution of genotype frequencies of regions across individuals.

Usage

plotGenotypesPerSNP(SNPhood.o, regions = NULL, fileToPlot = NULL,
  returnOnlyPlotNotObject = FALSE, verbose = FALSE)

Arguments

SNPhood.o	Object of class SNPhood
regions	Numeric or Character or NULL. Default NULL. Regions that should be plotted, either specified as integer (such as 1, value must be between 1 and the total number of regions as defined in the object) or their annotation (name must appear in the region names as obtained via the function annotationRegions). If set to NULL, all regions will be considered.
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 = plotGenotypesPerSNP(SNPhood.o, regions=1:20)

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