0.16.6 documentation

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

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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

Read BED intervals as ggchord features

On this page

• Usage
• Arguments
• Value
• Details
• See also
• Examples

Reads standard BED3 through BED12. Starts are converted from zero-based half-open intervals to one-based inclusive intervals; accession identifiers are kept verbatim. Blank lines, comments, and custom-track header lines are skipped. Every data row in a file must have the same number of fields. Zero-width insertion records cannot be represented as nonempty genomic intervals and produce an explicit error.

Usage

Code

read_bed(file = NULL, files = NULL, source_file = FALSE)

Arguments

file

Optional path vector or glob patterns; read before files.

files

Optional paths or wildcard patterns for multiple BED files.

source_file

Logical. Add a .source_file column, default FALSE.

Value

A feature data frame with accver, start, end, strand, directionality, original chromStart/chromEnd, optional BED fields, and .source_line (the physical file line). A ggchord_import attribute records the input/output coordinate conventions and files.

Details

BED names are labels, not guaranteed unique feature IDs. Unspecified strand remains "." and directionality = "none"; use geom_feature() for these records. Optional fields retain their BED names and coordinate conventions, including zero-based thickStart, thickEnd, and relative blockStarts. BED12 additionally creates a segments list-column of one-based inclusive block intervals after checking block counts, boundaries and non-overlap. Blocks are retained in genomic order on both strands. No colour or shape is inferred from BED display fields. BED extensions beyond column 12 require an explicit data-frame conversion with as_ggchord_feature().

See also

https://genome.ucsc.edu/FAQ/FAQformat.html#format1

ggchord_data_contract

Examples

Code

library(dplyr)
data(plasmid_example_pUC19)
feature_source <- find_common_features(plasmid_example_pUC19)
features <- feature_source |>
  select(accver, start, end, strand, type, anno)
bed <- tempfile(fileext = ".bed")
bed_rows <- features |>
  transmute(accver, start0 = start - 1L, end)
write.table(bed_rows, bed,
  sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE
)
read_bed(bed)
unlink(bed)