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Interactive browser for MitoPilot curation rulesets

Source: R/ruleset_browser.R
ruleset_browser.Rd

Generates a self-contained, interactive HTML visualization of the taxon-specific curation rulesets bundled with MitoPilot. The left side of the page is a collapsible taxonomy tree (you can scroll, expand, and collapse clades); the right side displays the curation rules for the currently selected clade.

Usage

ruleset_browser(
  output_file = tempfile(fileext = ".html"),
  open = interactive(),
  refresh_cache = FALSE,
  targets = NULL
)

Arguments

output_file

Path for the generated HTML file. Default is a temporary file. The file is fully self-contained (no external dependencies) and can be shared or embedded in documentation.

open

Logical, open the result in a browser when done? Default is interactive().

refresh_cache

Logical, ignore any cached NCBI lineages and re-fetch? Default FALSE.

targets

Optional character vector to limit the browser to a subset of rulesets (e.g. c("fish_mito", "bird_mito")). Default is all rulesets.

Value

(Invisibly) the path to the generated HTML file.

Details

The taxonomy backbone is built by querying NCBI's Taxonomy database (https://www.ncbi.nlm.nih.gov/taxonomy) for the full lineage of each ruleset's anchor clade and merging those lineages into a single tree. Each leaf in the tree corresponds to one MitoPilot ruleset (e.g. fish_mito). NCBI lineages are cached locally so repeat calls work offline.

Examples

if (FALSE) { # \dontrun{
# Build and open the ruleset browser
ruleset_browser()

# Save to a specific location without opening
ruleset_browser("MitoPilot_rulesets.html", open = FALSE)
} # }