Add an intervals panel to the browser — browser_add_intervals

Adds a panel that displays genomic intervals as rectangles (or arrows when show_direction = TRUE). The intervals can come from a misha intervals set, a file (BED/TSV), or an in-memory data frame.

Usage

browser_add_intervals_panel(
  browser,
  name,
  intervals = NULL,
  file = NULL,
  color = "grey60",
  outline_color = "grey20",
  color_by = NULL,
  colors = NULL,
  label_field = NULL,
  show_labels = FALSE,
  show_direction = FALSE,
  direction_field = "strand",
  filter_field = NULL,
  filter_values = NULL,
  filter_regex = NULL,
  height = NULL,
  y_title = NULL,
  ...
)

Arguments

browser: Browser object
name: Panel name
intervals: Intervals source. Either a character string naming a misha intervals set, or a data frame with chrom, start, end columns. When a data frame is supplied, the panel is runtime-only and is not serialized to YAML by browser_save_config().
file: Path to a BED/TSV file (used when intervals is not given).
color: Default fill color for intervals.
outline_color: Border color for rectangles.
color_by: Column to map to fill color.
colors: Named vector/list of colors keyed by color_by values.
label_field: Column to use for text labels.
show_labels: Whether to draw labels.
show_direction: Draw intervals as arrows by strand.
direction_field: Column name holding strand (default "strand").
filter_field: Column to filter on.
filter_values: Values to keep (vector).
filter_regex: Regex pattern to match.
height: Relative panel height.
y_title: Optional y-axis title.
...: Additional panel options.

Value

Updated browser object

Examples

if (FALSE) { # \dontrun{
df <- data.frame(
    chrom = "chr1",
    start = c(1e6, 1.2e6),
    end = c(1.05e6, 1.25e6),
    name = c("peak_a", "peak_b")
)
browser <- browser_create() %>%
    browser_add_intervals_panel(
        "peaks",
        intervals = df,
        label_field = "name",
        show_labels = TRUE
    )
} # }