0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

Site guide · find your task

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

Draw generic genomic features

On this page

• Usage
• Arguments
• Value
• Examples

A general layer for CDS, tRNA, rRNA, repeat, CRISPR, promoter or user-defined features. It supports directional arrows, blocks, notched chevrons and lollipops, all generated against the sequence's real local curve. Feature fill and geometry use independent role-specific scales.

Usage

Code

geom_feature(
  mapping = NULL,
  data = NULL,
  shape = "arrow",
  width = NULL,
  arrow_head_length = 0.04,
  arrow_head_width = 1,
  arrow_head_style = c("shouldered", "flush", "triangle"),
  short_feature = c("auto", "wedge", "block"),
  segment_boundaries = TRUE,
  boundary_colour = "#666666",
  boundary_linewidth = 0.25,
  boundary_linetype = "22",
  position = "identity",
  show.legend = TRUE,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping

Optional aesthetic mapping. Role aesthetics such as accver, start, end and strand may rename input columns; ordinary visual mappings are evaluated after geometry is generated.

data

data.frame with accver, start, end and strand; optional type, category and label. Factor start/end columns use their numeric labels, not their internal level codes. Coordinates must resolve to finite numbers. display_priority or logical prioritized_display. As an alternative to strand, directionality or direction may contain "forward", "reverse", "bidirectional", or "none".

shape

Fixed feature geometry. An explicitly supplied shape takes precedence over aes(feature_shape = ...): "arrow", "compact_arrow", "promoter_arrow", "primer_arrow", "marker", "block", "capped_line", "primer_arc", "chevron", or "lollipop". The default is "arrow". Use aes(feature_shape = type) together with scale_feature_shape_manual() to map categories to geometry.

width

Optional numeric/vector/list controlling width in the shared feature geometry engine. In a circular feature-label composition, the base width responds to final label size within bounded limits.

arrow_head_length, arrow_head_width

Arrow-head dimensions in the sequence-local frame, shared with geom_gene(). Values above one for arrow_head_width create a protruding block-arrow head.

arrow_head_style

Arrowhead construction: "shouldered" keeps the requested protruding head, "flush" keeps it level with the body, and "triangle" draws a full triangular wedge.

short_feature

Fallback for arrows too short to hold their requested head: an automatically compressed directional glyph, a wedge, or a block.

segment_boundaries

Draw explicit internal marks carried by a segmented feature. Contiguous source-segment joins use dotted dividers; a non-solid segment-level line_style may override them, while a cleavage_arrows coordinate adds or merges a biological cut mark. These marks never create additional arrowheads.

boundary_colour, boundary_linewidth, boundary_linetype

Appearance of internal segment joins.

position

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

show.legend, inherit.aes

Standard ggplot2 layer arguments.

...

Additional fixed polygon aesthetics.

Value

A ggplot2 layer.

Examples

Code

library(dplyr)
data(plasmid_example_pUC19)
seqs <- plasmid_example_pUC19 |>
  select(accver, length)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
# ASCII display copy for the default PDF help-example device.
features <- features |>
  mutate(anno = gsub("\u03b1", "alpha", anno, fixed = TRUE))
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(
    data = features,
    shape = "block"
  ) +
  coord_circular()