Plot a chord diagram of modification rewiring between conditions.

Display a circlize chord diagram showing position pairs where modification co-occurrence has changed between two conditions, based on the ratio of odds ratios (ROR). Chords are colored by direction: gained dependencies (positive log ROR) vs. lost dependencies (negative log ROR).

Usage

plot_chord_ror(
  ror_data,
  ror_cutoff = 0.5,
  gained_color = "#D55E00",
  lost_color = "#0072B2",
  sprinzl_coords = NULL,
  mods = NULL,
  title = NULL,
  transparency = 0.4
)

Arguments

ror_data

A tibble from compute_ror() with columns pos1, pos2, and log_ror.

ror_cutoff

Minimum absolute value of log_ror for a chord to be drawn. Default 0.5.

gained_color

Color for gained dependencies (positive log ROR). Default "#D55E00" (vermillion).

lost_color

Color for lost dependencies (negative log ROR). Default "#0072B2" (blue).

sprinzl_coords

An optional tibble from read_sprinzl_coords() used to order sectors and color by structural region.

mods

An optional tibble of modification annotations (e.g., from fetch_modomics_mods()) with columns pos and mod1. When provided along with sprinzl_coords, modification positions are highlighted as an annotation ring.

title

Optional plot title.

transparency

Transparency for chord colors. Default 0.4.

Value

invisible(NULL). Called for its side effect of producing a base graphics plot.

Examples

# \donttest{
results <- read_pipeline_results(
  clover_example("ecoli/config.yaml"),
  types = "odds_ratios"
)
or_data <- results$odds_ratios
or_data$condition <- ifelse(
  grepl("ctl", or_data$sample_id), "ctl", "inf"
)
ror <- compute_ror(or_data, numerator = "inf", denominator = "ctl")
plot_chord_ror(ror)

# }