Visualize Total CpGs at Different Coverage Cutoffs

plotCpGtotals() plots the number of CpGs remaining after filtering by different combinations of cov and perSample in a line plot and then saves it as a pdf.

Usage

plotCpGtotals(
  CpGtotals,
  nBreaks = 4,
  legend.position = c(1.08, 0.73),
  save = TRUE,
  file = "CpG_Totals.pdf",
  width = 11,
  height = 4.25,
  verbose = TRUE
)

Arguments

CpGtotals: A data.frame, output from getCpGtotals().
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

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

Examples

if (FALSE) {

# Read Bismark CpG Reports
colData <- read.xlsx("sample_info.xlsx", rowNames = TRUE)
bs <- getCpGs(colData, file = "Unfiltered_BSseq.rds")

# Examine CpG Totals at Different Cutoffs
CpGtotals <- getCpGtotals(bs, file = "CpG_Totals.txt")
plotCpGtotals(CpGtotals, file = "CpG_Totals.pdf")

# Filter BSseq Object
bs <- filterCpGs(bs, cov = 2, perSample = 0.75, file = "Filtered_BSseq.rds")
}