0.16.6 documentation

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Add a gene arrow layer

On this page

• Usage
• Arguments
• Value
• Examples

A directed-gene shortcut using the generic geom_feature() constructor with arrow geometry and the independent gene_fill role. Gene input still requires a known + or - strand; use geom_feature() for unknown strands. The gene fill scale is kept independent from the ribbon's fill scale via a separate internal aesthetic used by the ribbon layer.

Usage

Code

geom_gene(
  mapping = NULL,
  data = NULL,
  width = NULL,
  arrow_head_length = 0.04,
  arrow_head_width = 1,
  arrow_head_style = c("shouldered", "flush", "triangle"),
  short_feature = c("auto", "wedge", "block"),
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping

Default NULL (uses pre-computed data)

data

Default NULL (retrieved automatically from the layout)

width

Optional numeric/vector/list. Width of gene arrows, default 0.05

arrow_head_length, arrow_head_width

Shared arrow-head dimensions in the sequence-local frame.

arrow_head_style

Arrowhead construction: shouldered, flush, or a full triangular wedge.

short_feature

Fallback for arrows too short to hold their requested head: automatic wedge/block selection, a wedge, or a block.

position

Feature placement. Use "identity", "strand", "plasmid", position_strand(), position_plasmid(), or position_feature_stack().

show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional arguments passed to geom_polygon()

Value

A ggplot2 layer. To annotate the genes with their labels, add a geom_gene_label() layer.

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(gene_data_example)
genes <- gene_data_example |>
  transmute(accver, start, end, strand = source_strand)
ggchord(seq_data = seqs, gene_data = genes) +
  geom_seq() +
  geom_gene()