plotRegionTotals: Visualize Region Totals at Different Cutoffs

In cemordaunt/comethyl: An R Package for Weighted Region Comethylation Network Analysis

Visualize Region Totals at Different Cutoffs

Description

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.

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.

Value

A ggplot object.

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

## Not run: 

# 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")

## End(Not run)

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.