plotCpGtotals: Visualize Total CpGs at Different Coverage Cutoffs

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

Visualize Total CpGs at Different Coverage Cutoffs

Description

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.

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.

Value

A ggplot object.

See Also

• getCpGs() to generate the BSseq object from individual Bismark CpG reports.

• getCpGtotals() to generate CpGtotals.

• filterCpGs() to filter the BSseq object.

Examples

## Not run: 

# 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")

## End(Not run)

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