0.16.6 documentation

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

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

Clean ggchord input data with explicit, report-driven policies

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Applies a conservative, predictable set of cleaning policies to the three ggchord tables and returns the cleaned copies plus a full report. The original data frames are never modified. Nothing is dropped silently: every change (including every dropped row) is recorded in report with the original row number, the reason, the original value(s) and the new value(s). Its historical sorting default differs deliberately from preparation's direction-preserving default. Use reversed_interval = "keep" for directional links and circular-origin features; sorting endpoints loses information that a later workflow cannot reconstruct.

Usage

Code

clean_ggchord_data(
  seq_data,
  ribbon_data = NULL,
  gene_data = NULL,
  unknown_id = c("drop", "error", "keep"),
  out_of_range = c("clip", "drop", "error", "keep"),
  reversed_interval = c("sort", "drop", "error", "keep"),
  invalid_pident = c("clip", "drop", "error", "keep"),
  empty_annotation = c("keep", "drop", "replace"),
  replacement_annotation = "unannotated"
)

Arguments

seq_data

data.frame/tibble, required. Must contain accver and length; used as the coordinate reference for clipping. Reference IDs must always be non-missing, non-empty and unique, regardless of unknown_id.

ribbon_data

data.frame/tibble or NULL, optional. Alignment results. Other input types are rejected rather than treated as absent.

gene_data

data.frame/tibble or NULL, optional. Gene annotation data. Other input types are rejected rather than treated as absent.

unknown_id

Character, default "drop". Policy for rows whose sequence ID in ribbon_data or gene_data is missing, empty or unknown: "drop" removes them, "error" stops with a message, "keep" leaves them unchanged. A kept row without a reference sequence is reported, but its coordinates and annotations are not cleaned and it is not guaranteed to be drawable. IDs are never guessed or replaced. Other structural checks, including finite numeric coordinates and valid gene strands, still apply.

out_of_range

Character, default "clip". Policy for coordinates outside [1, sequence length]: "clip" clamps them, "drop" removes the row, "error" stops, "keep" leaves them unchanged. Coordinates are one-based inclusive, so start == end is a valid single-base interval and is retained. With "clip", intervals wholly outside their sequence are removed and reported; partially overlapping intervals retain their intersection, even a single base.

reversed_interval

Character, default "sort". Policy for intervals with start > end: "sort" swaps the endpoints so the feature draws stably (the original direction is recorded in the report), "drop" removes the row, "error" stops, "keep" leaves them unchanged.

invalid_pident

Character, default "clip". Policy for pident outside [0, 100]: "clip" clamps them, "drop" removes the row, "error" stops, "keep" leaves them unchanged.

empty_annotation

Character, default "keep". Policy for missing/empty anno in gene data: "replace" fills them with replacement_annotation, "drop" removes the row, "keep" leaves them unchanged.

replacement_annotation

Character, default "unannotated". Replacement annotation used when empty_annotation = "replace".

Value

A list with four components: seq_data, ribbon_data, gene_data (cleaned copies) and report (a data.frame with columns table, row (original row number), column, reason, original_value, new_value and action).

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(seq_data_example)
seqs <- seq_data_example |>
  select(accver, length)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
# Deliberate diagnostic error in a copy; source observations remain unchanged.
problem <- links |>
  slice_head(n = 2) |>
  mutate(qaccver = replace(qaccver, 2, "absent"))
cleaned <- clean_ggchord_data(seqs, problem, unknown_id = "drop")
cleaned$report