Plot Manhattan-Style View of DMR Scores — plotDMRsManhattan • CMEnt

Creates a Manhattan-style genome-wide scatter plot of DMR scores. DMRs are colored by their dominant genomic region class inferred from DMR annotations.

Usage

plotDMRsManhattan(
  dmrs,
  region = NULL,
  genome = "hg38",
  promoter_col = "in_promoter_of",
  gene_body_col = "in_gene_body_of",
  point_size = 1.1,
  point_alpha = 0.75,
  block_col = "block_id",
  show_blocks = TRUE,
  block_alpha = 0.12,
  block_linewidth = 0.25,
  output_file = NULL,
  width = 12,
  height = 6
)

Arguments

dmrs: GRanges object or data frame. DMR results from buildDMRs.
region: Optional plotting scope. Can be NULL for full-chromosome plotting, a GRanges, a string in the form "chr:start-end", or a data.frame/list with chr, start, and end.
genome: Character. Genome version passed to .convertToGRanges (default: "hg38").
promoter_col: Character. Metadata column indicating promoter overlap (default: "in_promoter_of").
gene_body_col: Character. Metadata column indicating gene-body overlap (default: "in_gene_body_of").
point_size: Numeric. Point size (default: 1.1).
point_alpha: Numeric. Point alpha in [0, 1] (default: 0.75).
block_col: Character. Metadata column containing block IDs (default: "block_id").
show_blocks: Logical. If TRUE, draw translucent rectangles for identified blocks (default: TRUE).
block_alpha: Numeric. Alpha for block rectangles in [0, 1] (default: 0.12).
block_linewidth: Numeric. Line width for block rectangle borders (default: 0.25).
output_file: Character or NULL. If non-NULL, path to save the plot as a PDF (default: NULL).
width: Numeric. Width of the output PDF in inches (default: 12).
height: Numeric. Height of the output PDF in inches (default: 6).

Value

A ggplot object.

Examples

dmrs <- data.frame(
    chr = c("chr1", "chr1", "chr2"),
    start = c(100, 200, 100),
    end = c(150, 250, 150),
    score = c(0.6, 0.8, 0.7)
)
p <- plotDMRsManhattan(dmrs)