plotClusterAverage: Visualize average enrichment per cluster

Description Usage Arguments Value See Also Examples

View source: R/visualize.R


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


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



Object of class SNPhood


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.


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).


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.


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)


Logical(1). Default FALSE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?


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



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

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