parse_plot_params: Parse raw UI / CLI strings into structured plot parameters

In Rclade: Automated Deep-Time Phylogenetic Tree Collapsing and Visualization

Parse raw UI / CLI strings into structured plot parameters

Description

This is the ONLY place that converts raw UI strings (comma-separated highlight lists, "A:#FF0000,B:#00FF00" color mappings, "k:k,ss:ss" taxonomy level specs, "auto"/"tab"/"comma" separators) into the structured R objects expected by plot_timetree().

Usage

parse_plot_params(
  color_mapping = NULL,
  taxonomy_levels = NULL,
  highlight = NULL,
  taxonomy_file_sep = "auto"
)

Arguments

color_mapping	Character string "GroupA:#FF0000,GroupB:#00FF00", or an already-structured named vector/list. A single bare hex ("#FF0000") is returned as a length-1 color vector (M-E2 / L-D7). NULL -> NULL.
taxonomy_levels	Character string "k:k,ss:ss", or a pre-built list(codes=, names=). NULL -> NULL.
highlight	Character string "LUCA, LACA", or a character vector. NULL -> NULL.
taxonomy_file_sep	One of "auto", "tab", "comma", or an already-resolved separator (a literal tab, ",", or "auto").

Details

Both the CLI (build_plot_timetree_params) and the Shiny server() must route their raw inputs through this function so that parsing logic lives in exactly one location.

Value

A named list with components:

color_mapping	named character vector or NULL
taxonomy_levels	list(codes, names) or NULL
highlight	character vector or NULL
taxonomy_file_sep	character scalar

Rclade documentation built on Sept. 26, 2026, 5:07 p.m.