Add an automatically arranged gene label layer — geom_gene_label

Like geom_gene_label(), but labels are placed by one of three deterministic collision-avoiding layouts. The default "aligned" layout uses orderly cardinal rails, "radial" uses compact local offset tracks, and "arc" keeps text close to and rotated with the sequence curve.

Usage

geom_gene_label_repel(
  mapping = NULL,
  data = NULL,
  gene_label_layout = "aligned",
  gene_label_size = NULL,
  gene_label_wrap = NULL,
  gene_label_side = "outside",
  max_overlaps = Inf,
  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_layout: Character, default "aligned". Label layout: "aligned" uses horizontal labels on orderly top, bottom, left and right rails; "radial" uses horizontal labels on the nearest collision-free local offset track; "arc" rotates labels along the sequence tangent and keeps them close to their genes.
gene_label_size: Numeric. Label font size, default 2.5
gene_label_wrap: Numeric or NULL, default NULL. When set, long gene annotations are wrapped at this many characters (e.g. 15).
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).
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.
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).

Details

The local outside/inside label concepts are informed by SnapGene and Geneious, but ggchord uses generic mode names and an independent geometry implementation. See SnapGene feature labels and Geneious label options.

Low-level force, padding, orientation and segment arguments used by earlier releases have been removed and now produce an error. Use gene_label_layout for automatic placement, or geom_gene_label() for manual rotation and offsets.

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