Is it possible to increase the data marker size for PlotDenoisedCopyRatios? The markers are rather small and difficult to visualize when plotting data where the coverage isn't very dense.
The short answer is no. PlotDenoisedCopyRatios does not expose the types of R features that allow you to change how the data is visualized. Your best bet for customization is to import and visualize the data, e.g. into RStudio, yourself. You can get a jump start by referencing the PlotDenoisedCopyRatios.R script the tool uses. The markers are intentionally small to accommodate dense WGS data.