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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

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Filter alignment ribbons before plotting

On this page

• Usage
• Arguments
• Value
• See also
• Examples

Keeps the ribbon rows that satisfy all requested criteria and optionally sorts them. The returned data frame keeps every extra column and the original column order; the original row numbers are attached as the source_rows attribute. Each non-NULL numeric threshold must be one finite number. Columns used by a numeric criterion must be numeric; missing values fail that criterion.

Usage

Code

filter_ggchord_ribbons(
  ribbon_data,
  seq_ids = NULL,
  min_pident = NULL,
  max_pident = NULL,
  min_length = NULL,
  max_evalue = NULL,
  min_bitscore = NULL,
  min_query_coverage = NULL,
  min_subject_coverage = NULL,
  keep_pairs = NULL,
  drop_self_links = TRUE,
  sort_by = NULL
)

Arguments

ribbon_data

data.frame with at least qaccver and saccver columns (normally the full ribbon_data format).

seq_ids

Optional character vector. Keep only rows where both the query and the subject are in seq_ids.

min_pident, max_pident

Optional numeric. Lower/upper bounds on pident.

min_length

Optional numeric. Lower bound on length.

max_evalue

Optional numeric. Upper bound on evalue (requires an evalue column).

min_bitscore

Optional numeric. Lower bound on bitscore (requires a bitscore column).

min_query_coverage

Optional numeric (0-100). Lower bound on the query coverage. Uses the qcovs column when present; otherwise computed from qlen and the query interval (requires qlen).

min_subject_coverage

Optional numeric (0-100). Lower bound on the subject coverage, computed from slen and the subject interval (requires an slen column).

keep_pairs

Optional data.frame/list/matrix describing an undirected set of sequence pairs. A data.frame or matrix with the first two columns used as query/subject IDs, or a list of length-2 character vectors. A row is kept when its query/subject pair matches any pair in either direction.

drop_self_links

Logical, default TRUE. Remove rows where qaccver == saccver.

sort_by

Optional character vector of column names. Prefix a name with "-" or "desc:" for descending order (e.g. c("pident", "-evalue")).

Value

A list with data (the filtered data frame, with source_rows attribute) and report (n_input/n_kept/n_removed, removed_by_reason, removed_rows and kept_rows).

See also

ggchord_data_contract

Examples

Code

library(dplyr)
data(ribbon_data_example)
links <- ribbon_data_example |>
  select(qaccver, saccver, qstart, qend, sstart, send, pident, length)
out <- filter_ggchord_ribbons(links, min_pident = 95, min_length = 500)
out$report