0.16.6 documentation

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

Terminology and design sources

On this page

• Shared terminology
• Design and asset provenance

Shared terminology

English	现代汉语	API / units
sequence	序列	accver / length
chord diagram	弦图	coord_chord()
circular sequence map	单序列圆图	coord_circular()
collinearity plot	共线性图	coord_collinear()
interval link / ribbon	区间连接 / 连接带	qaccver / saccver
feature	通用注释特征（feature）	geom_feature()
gene	已知链的基因	geom_gene()
strand	链方向	+ / - / unknown
aesthetic mapping	美学属性映射	aes()
scale	标度	scale_*()
guide	图例 / 标度指南	guides()
position	局部位置调整	position_*()
track	定量轨道	position_track()
genomic position	基因组位置	one-based inclusive bp / 一基闭区间
layout units	原生布局单位	not bp or mm / 不等于 bp 或 mm
source row	已解析输入来源行	source_row
physical file line	物理文件行	.source_line
focus	局部聚焦	focus_ggchord_data()
segment	分段窗口	segment_ggchord_data()
leader	标签引导线	label / connection
CDS projection	编码序列坐标投影	build_ggchord_cds()
measured panel	已测量面板	not visual certification / 不等于视觉认证

Design and asset provenance

The grammar follows ggplot2: mappings, scales, geometry, positions, coordinates and themes retain distinct responsibilities. Compact query/subject field names follow BLAST-style tables; ggchord does not run an alignment tool during drawing. Circular hierarchy and feature readability are compared with Circos, clinker and DNA Features Viewer, as recorded in the repository design documents. These are conceptual comparisons, not copied APIs.

The detailed ggchord artwork was supplied by the user on 2026-11-01 for this website and documentation. Full-size PNG and WebP preserve every decoded RGBA pixel. Only the small navigation thumbnail is resized. See the image manifest for source hashes and exact sizes. The compact hexagonal study mark below, site CSS/JS and documentation diagrams are original project assets under the repository MIT terms. The study mark is supplementary, not a replacement for the supplied artwork.

System fonts are used; no webfont, icon library or third-party image is downloaded. Plot colours come from the package’s existing defaults or explicit teaching code; those literal colour choices are listed with the source. The site uses the existing Pandoc and R documentation converters at build time without bundling their binaries or stylesheets.