Plot Multiple DMRs in a Grid — plotDMRs • CMEnt

Creates a grid of DMR plots for multiple regions. Can optionally include beta value heatmaps if beta and pheno data are provided.

Usage

plotDMRs(
  dmrs,
  dmr_indices = NULL,
  top_n = 4,
  score_by = c("delta_beta", "score"),
  beta = NULL,
  pheno = NULL,
  sample_group_col = NULL,
  genome = NULL,
  array = NULL,
  beta_locs = NULL,
  ncol = 1,
  output_file = NULL,
  width = 8,
  height = 12,
  ...
)

Arguments

dmrs: GRanges object. Output from buildDMRs.
dmr_indices: Integer vector. Which DMRs to plot. If NULL, selects top_n DMRs using score_by.
top_n: Integer. Number of top DMRs to plot when dmr_indices is NULL (default: 4).
score_by: Character. Which metric to use for ranking DMRs when dmr_indices is NULL. Options: "delta_beta" or "score" (default: "delta_beta").
beta: BetaHandler object, character path to beta file, or beta values matrix (optional). If provided, creates plots with heatmaps.
pheno: Data frame or character path to phenotype file (optional). Required when beta is provided.
sample_group_col: Character. Required column in pheno for sample grouping when pheno is provided.
genome: Character. Genome version. Required for data.frame DMRs; inferred from GRanges seqinfo when available.
array: Character. Array platform type. Required when beta row names are array probe IDs and beta_locs is not provided.
beta_locs: Data frame. Genomic locations sorted by position (optional). If NULL, will be fetched based on array and genome.
ncol: Integer. Number of columns in the grid (default: 1).
output_file: Character. Path to save the combined plot as PDF (optional). If NULL, the plot is not saved to file.
width: Numeric. Width of the output PDF in inches (default: 8).
height: Numeric. Height of the output PDF in inches (default: 12).
...: Additional arguments passed to plotDMR.

Value

If beta is NULL: A gtable object. If beta is provided: A list of combined plot objects with structure and heatmap.

Examples

dmrs <- readRDS(system.file(
    "extdata", "example_outputChr5And11.rds", package = "CMEnt"
))
if (requireNamespace(
    "IlluminaHumanMethylation450kanno.ilmn12.hg19", quietly = TRUE
)) {
    plotDMRs(dmrs, dmr_indices = seq_len(min(2, length(dmrs))),
             array = "450K", ncol = 2, plot_motif = FALSE)
}