Visualize Region Totals at Different Cutoffs

plotRegionTotals() plots the total number of regions, width, and total number of CpGs remaining after filtering by different combinations of covMin and methSD in a line plot and then saves it as a .pdf.

Usage

plotRegionTotals(
  regionTotals,
  nBreaks = 4,
  legend.position = c(1.08, 0.897),
  save = TRUE,
  file = "Region_Totals.pdf",
  width = 11,
  height = 11,
  verbose = TRUE
)

Arguments

regionTotals

A data.frame, output from getRegionTotals().

nBreaks

A numeric(1) specifying the number of breaks used for both axes and the legend.

legend.position

A numeric(2) specifying the position of the legend, as x-axis, y-axis. May also be a character(1) indicating "none", "left", "right", "bottom", or "top".

save

A logical(1) indicating whether to save the plot.

file

A character(1) giving the file name (.pdf) for the saved plot.

width

A numeric(1) specifying the width in inches of the saved plot.

height

A numeric(1) specifying the height in inches of the saved plot.

verbose

A logical(1) indicating whether messages should be printed.

Value

A ggplot object.

Details

plotRegionTotals() is designed to be used in combination with getRegionTotals(). A ggplot object is produced and can be edited outside of this function if desired.

See also

• getRegions() to generate the set of regions.

• plotRegionStats(), plotSDstats(), and getRegionTotals() for more help visualizing region characteristics and setting cutoffs for filtering.

• filterRegions() for filtering regions by minimum coverage and methylation standard deviation.

Examples

if (FALSE) {

# Call Regions
regions <- getRegions(bs, file = "Unfiltered_Regions.txt")
plotRegionStats(regions, maxQuantile = 0.99,
                file = "Unfiltered_Region_Plots.pdf")
plotSDstats(regions, maxQuantile = 0.99,
            file = "Unfiltered_SD_Plots.pdf")

# Examine Region Totals at Different Cutoffs
regionTotals <- getRegionTotals(regions, file = "Region_Totals.txt")
plotRegionTotals(regionTotals, file = "Region_Totals.pdf")

# Filter Regions
regions <- filterRegions(regions, covMin = 10, methSD = 0.05,
                         file = "Filtered_Regions.txt")
plotRegionStats(regions, maxQuantile = 0.99,
                file = "Filtered_Region_Plots.pdf")
plotSDstats(regions, maxQuantile = 0.99,
            file = "Filtered_SD_Plots.pdf")
}