Plot Circos Visualization of DMRs — plotDMRsCircos • CMEnt

Creates a circular genome plot using circlize showing DMRs with multiple tracks: ideogram track with chromosome bands, DMR arcs colored by delta beta, beta value heatmaps for each sample, and motif-based interaction links between DMRs.

Usage

plotDMRsCircos(
  dmrs,
  beta = NULL,
  pheno = NULL,
  genome = NULL,
  array = NULL,
  sorted_locs = NULL,
  components = NULL,
  interactions = NULL,
  sample_group_col = NULL,
  min_similarity = 0.8,
  motif_site_flank_size = 5,
  max_num_samples_per_group = 5,
  max_dmrs_per_chr = 10,
  max_sites_per_dmr = 5,
  min_component_size = 2,
  max_components = 30,
  chromosomes = NULL,
  region = NULL,
  query_components_with_jaspar = TRUE,
  unmatched_interaction_color = "#B3B3B3",
  group_colors = NULL,
  low_beta_color = "#2b83ba",
  mid_beta_color = "#f7f7f7",
  high_beta_color = "#d7191c",
  neg_delta_color = "#055709",
  zero_delta_color = "#f0ec10",
  pos_delta_color = "#801414",
  legend_width_ratio = 0.5,
  degenerate_resolution = 1e+06,
  output_file = NULL,
  verbose = NULL
)

Arguments

dmrs: GRanges object or data frame. DMR results from buildDMRs.
beta: BetaHandler object, character path to beta file, or beta values matrix. If not provided, beta heatmap track will be omitted.
pheno: Data frame or character path to phenotype file. Sample information with rownames matching beta column names (required for beta track, if not provided beta track will not be shown).
genome: Character. Required if DMRs are provided as a data frame or they lack seqinfo.
array: Character. Array platform type (e.g., "EPIC", "450K"). Required if beta is provided as a file path and is indexed by array probe IDs.
sorted_locs: Data frame. Genomic locations sorted by position (optional). If NULL, will be fetched based on array and genome.
components: Data frame. Output from motif component detection (optional, will be computed if missing).
interactions: Data frame. Output from motif interaction detection (optional, will be computed if missing).
sample_group_col: Character. Required column in pheno for sample grouping when pheno is provided.
min_similarity: Numeric. Minimum motifs PWM similarity threshold for considering DMRs are related (default: 0.8).
motif_site_flank_size: Integer. Flanking region size for motif extraction in bp (default: 5).
max_num_samples_per_group: Integer. Maximum number of samples to show per group in heatmap (default: 5).
max_dmrs_per_chr: Integer. Maximum number of DMRs to use per chromosome (default: 10). The DMRs with highest absolute delta beta will be selected.
max_sites_per_dmr: Integer. Maximum number of sites to show per DMR in scatter/heatmap (default: 5).
min_component_size: Integer. Minimum motif component size to retain (default: 2).
max_components: Integer. Maximum number of interactions to plot (default: 30).
chromosomes: Character vector. Subset of chromosomes to display (default: NULL, show all available).
region: Genomic region to display. Can be NULL, a GRanges, a string in the form chr:start-end, or a data.frame/list with columns chr, start, end.
query_components_with_jaspar: Logical. Whether computed motif components should be queried against JASPAR before plotting (default: TRUE). Set to FALSE to keep link computation cheaper.
unmatched_interaction_color: Character. Color used for interaction components without JASPAR matches. These links are shown but omitted from the interaction legend (default: "#B3B3B3").
group_colors: Named character vector of colors for sample groups labels in the beta values track (names should match unique values in pheno[[sample_group_col]]). If not provided, default colors will be used.
low_beta_color: Character. Color for low beta values in the heatmap (default: "#2b83ba").
mid_beta_color: Character. Color for mid beta values in the heatmap (default: "#f7f7f7").
high_beta_color: Character. Color for high beta values in the heatmap (default: "#d7191c").
neg_delta_color: Character. Color for negative delta beta values in the DMR arcs (default: "#055709").
zero_delta_color: Character. Color for zero delta beta values in the DMR arcs (default: "#f7f7f7").
pos_delta_color: Character. Color for positive delta beta values in the DMR arcs (default: "#801414").
legend_width_ratio: Numeric. Fraction of horizontal canvas reserved for legends (default: 0.50).
degenerate_resolution: Integer. Resolution in base pairs for simplifying narrow glyphs: link ribbons are drawn as lines when both anchors are below this span, and DMR arcs are drawn as lines instead of rectangles below this span (default: 1e6).
output_file: Character or NULL. Optional PDF path for the plot.
verbose: Numeric. Optional verbosity override.

Value

NULL invisibly after drawing the plot.

Examples

dmrs <- readRDS(system.file(
    "extdata", "example_outputChr5And11.rds", package = "CMEnt"
))
plotDMRsCircos(dmrs, query_components_with_jaspar = FALSE)