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

Read one or more GFF3 files into gene_data format

On this page

• Usage
• Arguments
• Value
• See also
• Examples

file reads a single GFF3 file; files reads multiple files at once and combines them. files accepts a character vector of literal paths and/or wildcard patterns (e.g. "examples/gff3/*.gff3").

Usage

Code

read_gff3(
  file = NULL,
  files = NULL,
  feature_types = "CDS",
  anno_from = c("product", "Name", "gene", "ID"),
  unstranded = c("plus", "drop", "keep"),
  source_file = FALSE
)

Arguments

file

Optional path vector or glob patterns; read before files.

files

Optional character vector of GFF3 files (literal paths and/or wildcard patterns). All matched files are read and combined.

feature_types

Character vector of feature types to keep, default "CDS".

anno_from

Character vector of GFF3 attribute keys, tried in order to fill the anno column.

unstranded

"plus" (legacy default) assigns unknown strands to +; "drop" removes them. Use "keep" with geom_feature() to retain them as nondirectional . intervals. source_strand always records the input.

source_file

Logical. Add a .source_file column when reading one or more files, default FALSE.

Value

A data.frame with accver, start, end, strand, anno followed by type, source, score, phase, attributes, source_strand, feature_id (decoded GFF3 ID, or missing) and a parent_ids list-column. Repeated IDs for discontinuous features and multiple parents are retained; selecting feature types may omit parents. A ggchord_import attribute records files, per-file output row counts and the one-based inclusive coordinate convention.

See also

ggchord_data_contract

Examples

Code

if (FALSE) { # \dontrun{
library(dplyr)
# Requires the source checkout or tutorial input bundle.
source <- read_gff3("examples/gff3/MT108731.1.gff3", unstranded = "keep")
features <- source |>
  select(accver, start, end, strand, anno)
} # }