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Plot DMR

Source: R/plot_dmrs.R
plotDMR.Rd

Creates a detailed DMR plot with an integrated heatmap showing beta values across samples for seeds and surrounding sites. The plot consists of two panels: the top panel shows the DMR structure with seeds and extended sites, and the bottom panel displays a heatmap of beta values for all samples, if beta values are provided. Additionally, if motif information is available or can be extracted, a sequence logo plot is added showing the nucleotide composition and information content around site sites in the DMR.

Usage

plotDMR(
  dmrs,
  dmr_index,
  beta = NULL,
  pheno = NULL,
  genome = "hg38",
  array = c("450K", "27K", "EPIC", "EPICv2"),
  beta_locs = NULL,
  sample_group_col = "Sample_Group",
  extend_by_dmr_size_ratio = 0.2,
  min_extension_bp = 50,
  max_sites = 100,
  max_samples_per_group = 10,
  plot_motif = TRUE,
  motif_site_flank_size = 5,
  plot_title = TRUE,
  output_file = NULL,
  width = 8,
  height = 12
)

Arguments

dmrs

GRanges object. Output from buildDMRs.

dmr_index

Integer. Which DMR to plot.

beta

BetaHandler object, character path to beta file, or beta values matrix. If a character path or matrix is provided, a BetaHandler will be created automatically.

pheno

Data frame or character path to phenotype file. Sample information with rownames matching beta column names (required).

genome

Character. Genome version (default: "hg38").

array

Character. Array platform type. Must be NULL if input is not array-based. Ignored if beta_locs is provided. (default: "450K")

beta_locs

Data frame. Genomic locations sorted by position (optional).

sample_group_col

Character. Column in pheno for sample grouping (default: "Sample_Group").

extend_by_dmr_size_ratio

Numeric. Ratio of the DMR width to extend the plot region outside of the DMR in both sides (default: 0.2).

min_extension_bp

Integer. Minimum extension in base pairs (default: 50).

max_sites

Integer. Maximum number of sites to show in heatmap (default: 100).

max_samples_per_group

Integer. Maximum number of samples to show per group in heatmap (default: 10).

plot_motif

Logical. Whether to plot the sequence logo motif (default: TRUE).

motif_site_flank_size

Integer. Number of base pairs to include as flanking regions around each site site for motif extraction (default: 5).

plot_title

Logical. Whether to display the title on the plot. If FALSE, the title is shown in the logs (default: TRUE).

output_file

Character. If provided, saves the plot to the specified file path (PDF format).

width

Numeric. Width of the output PDF in inches when output_file is provided (default: 8).

height

Numeric. Height of the output PDF in inches when output_file is provided (default: 12).

Value

A combined plot object (gridExtra) containing the DMR structure plot, beta values heatmap (if beta is provided), and sequence logo motif plot (if motif information is available and plot_motif is TRUE).

Examples

dmrs <- readRDS(system.file(
    "extdata", "example_outputChr5And11.rds", package = "CMEnt"
))
# \donttest{
plotDMR(dmrs, 1, plot_motif = FALSE)
# }