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

Convert intervals to generic ggchord features

On this page

• Usage
• Arguments
• Value
• See also
• Examples

GRanges coordinates are already one-based inclusive and are not shifted. Strand * is retained as source_strand, while the output uses strand = "." and directionality = "none". Use the returned table in geom_feature(data = ...) to preserve nondirectional intervals; geom_gene() requires directional gene input. No unknown strand is invented as +.

Usage

Code

as_ggchord_feature(x, mapping = NULL)

Arguments

x

A data frame or GRanges object.

mapping

Optional named character vector mapping output roles to source columns, as in as_ggchord_seq().

Value

An ordinary feature data frame with accver, start, end, strand, directionality, retained metadata and conversion provenance. Conflicting metadata names receive a metadata_ prefix; the attribute's column_map records the output name.

See also

ggchord_data_contract

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)
renamed <- genes |>
  rename(chrom = accver, left = start, right = end)
features <- as_ggchord_feature(renamed,
  mapping = c(accver = "chrom", start = "left", end = "right")
)
ggchord(seq_data = seqs) +
  geom_seq() +
  geom_feature(data = features)