Draw generic genomic features — geom

A thin, backwards-compatible convenience layer for CDS, tRNA, rRNA, repeat, CRISPR, promoter or user-defined features. It prepares a gene-compatible table from a type / category / label specification and reuses the proven geom_gene() geometry and scales.

Usage

geom_feature(
  data,
  type = "type",
  category = NULL,
  label = "label",
  feature_colors = NULL,
  feature_width = NULL,
  feature_offset = NULL,
  feature_order = NULL,
  show_legend = TRUE,
  legend_position = "right",
  ...
)

Arguments

data: data.frame with seq_id, start, end and strand; optional type, category and label.
type: Column name used as the feature type, default "type".
category: Optional column name used for colour grouping; defaults to type.
label: Optional column name used for annotation text; defaults to label when present, otherwise type.
feature_colors: Optional named color vector by feature value; unnamed vectors are recycled positionally.
feature_width: Optional numeric or named vector controlling feature width; passed to geom_gene(gene_width = ...).
feature_offset: Optional numeric or named vector controlling feature offset; passed to geom_gene(gene_offset = ...).
feature_order: Optional feature order for the legend.
show_legend: Logical. Show the feature legend, default TRUE.
legend_position: Position of the feature legend: "left", "right", "top", "bottom" or "inside".
...: Additional arguments passed to geom_gene().

Value

A list of ggplot2 layers

Examples

library(ggchord)
data(seq_data_example)
features <- data.frame(seq_id = "MT108731.1",
                       start = 1000, end = 4000,
                       strand = "+", type = "CDS")
p <- ggchord(seq_data_example) + geom_seq() + geom_feature(features)
p