Add a repelled gene label layer (ggrepel-style) — geom_gene_label

Like geom_gene_label(), but the labels are placed with a force-based simulation that pushes them away from the genes and from each other (similar to ggrepel::geom_text_repel()). Labels that move far enough from their anchor are connected to it with a leader line, and labels that still overlap too many others can be hidden.

Usage

geom_gene_label_repel(
  mapping = NULL,
  data = NULL,
  gene_label_size = NULL,
  gene_label_rotation = NULL,
  gene_label_radial_offset = NULL,
  gene_label_circum_offset = NULL,
  gene_label_circum_limit = NULL,
  gene_label_wrap = NULL,
  max_overlaps = Inf,
  box_padding = 0.25,
  point_padding = 0.1,
  min_segment_length = 0.05,
  force = 1,
  seed = 123,
  gene_label_orientation = "horizontal",
  gene_label_segment = "elbow",
  gene_label_side = "outside",
  gene_label_segment_linetype = "auto",
  show_legend = FALSE,
  ...
)

Arguments

mapping: Default NULL (uses pre-computed data)
data: Default NULL (retrieved automatically from the layout)
gene_label_size: Numeric. Label font size, default 2.5
gene_label_rotation: Optional numeric/vector/list. Label rotation angle, default 0
gene_label_radial_offset: Optional numeric/vector/list. Radial offset of labels, default 0
gene_label_circum_offset: Optional numeric/vector/list. Circumferential offset of labels, default 0
gene_label_circum_limit: Optional logical/vector/list. Whether to limit circumferential offset, default TRUE
gene_label_wrap: Numeric or NULL, default NULL. When set, long gene annotations are wrapped at this many characters (e.g. 15).
max_overlaps: Numeric, default Inf. Hide labels that still overlap more than this many other labels after repulsion (ggrepel-style decluttering). Use a finite value to clean up crowded plots.
box_padding: Numeric, default 0.25. Extra padding around each label box (data units).
point_padding: Numeric, default 0.1. Extra padding around the anchor points (data units).
min_segment_length: Numeric, default 0.05. Labels that moved less than this distance (data units) from their anchor do not draw a leader line. Keep it small so that every label is connected to its gene.
force: Numeric, default 1. Strength of the repulsive forces.
seed: Numeric, default 123. Random seed for reproducibility.
gene_label_orientation: Character, default "horizontal". One of "arc" (text rotated along the sequence arc) or "horizontal" (all labels are drawn horizontally).
gene_label_segment: Character, default "elbow". Leader line style: a straight "line" from the gene to the label, or an L-shaped "elbow" (a short segment outward, then a horizontal segment to the label). Elbow segment lengths adapt to each label's position and text width, so labels can be placed freely.
gene_label_side: Character, default "outside". Which side of the arc the labels sit on. "auto" keeps the strand-based placement (same as before); "outside" moves labels that would be inside the chord (where they can overlap the ribbons) to the outside of their arc; "inside" does the opposite. Labels moved to the other side are connected with a dashed leader line (see gene_label_segment_linetype).
gene_label_segment_linetype: Character or numeric, default "auto". Leader-line linetype. "auto" draws solid lines, except for labels that were moved to the other side of their arc, which are drawn dashed. Any other valid ggplot2 linetype (e.g. "solid", "dashed", "dotted", or a numeric dash pattern) is used for all leader lines.
show_legend: Whether to show the legend, default FALSE
...: Additional arguments passed to geom_text()

Value

A list of ggplot2 layers (a leader-line layer and a text layer).

Examples

library(ggchord)
data(seq_data_example)
data(gene_data_example)
p <- ggchord(seq_data_example, gene_data = gene_data_example) +
  geom_seq() + geom_gene() + geom_gene_label_repel()
p