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

1.1 Tables and field meanings

On this page

• Minimal shapes of three tables
• Names and optional columns
• Inspect real tables
• Coordinates and directions

Learn the tables before selecting layers. Chord comparison was ggchord’s original core view. Its early BLAST workflows explain the compact field names retained today. A multi-sequence chord view displays existing interval comparisons among sequences; drawing does not run a multiple-sequence alignment algorithm.

Minimal shapes of three tables

Table	Required columns	One row represents
seq_data	accver, length	One sequence and its full length in bp
ribbon_data	qaccver, saccver, qstart, qend, sstart, send	One observed pair of aligned intervals
gene_data	accver, start, end, strand	One directed gene interval

Backbones alone need neither links nor genes. Use geom_feature() for annotations with unknown strand rather than assigning a direction.

Names and optional columns

accver originated from accession.version, but any stable contig identifier is allowed; versions are not added or removed. q means query and s means subject. Both IDs must occur in the sequence table.

pident is percentage identity, needed only for identity mapping/filtering. Alignment length differs from full sequence length. Keep evalue, bitscore, qlen and slen when required by an analysis. Gene anno is optional annotation text; supply it for labels. Additional category columns can feed aes() without becoming mandatory inputs.

Inspect real tables

Code

library(ggchord)
library(dplyr)
seq_data_example |> select(accver, length) |> slice_head(n = 3)
ribbon_data_example |> select(qaccver, saccver, qstart, qend, sstart, send) |> slice_head(n = 3)
gene_data_example |> transmute(accver, start, end, strand = source_strand, anno) |> slice_head(n = 3)

These are bundled source-backed records. This historical teaching fixture stores biological strand separately in source_strand; restore it explicitly. Newly read GFF3 annotations use their ordinary strand column.

Coordinates and directions

Use one-based inclusive bp coordinates. Genes have ordered bounds with a separate strand. Endpoint order can represent reverse alignments; do not sort every link. Maximum feature endpoints do not establish full sequence lengths. See the coordinate contract.

Continue to 1.2 From analysis results to input tables.