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Run simpleTaxonomy Shiny App

Source: R/shiny.R
run_taxonomy.Rd

Run the simple shiny app that is included with simpleTaxonomy. The app provides several features to interact with a taxonomy_graph. A taxonomy_graph can be read from a file or an URL. By default, the app loads the data from https://github.com/stibu81/taxonomyData.

Usage

run_taxonomy(
  file = NULL,
  root = NULL,
  expand_ranks = c("Gattung", "Art", "Unterart"),
  image_size = 150,
  link_length = 200,
  launch_browser = NULL
)

Arguments

file

Path to a file containing a taxonomy_graph. If omitted, the data from https://github.com/stibu81/taxonomyData is used.

root

character giving the common or scientific name of the taxon to select as root. If omitted, the actual root of the taxonomy graph is used. If the selected root does not exist in the graph, the app also falls back on the actual root of the graph.

expand_ranks

a list of ranks that should always be expanded. This can be changed interactively in the app.

image_size

numeric giving the default image width in pixels used in the app. The user can change this interactively in the app.

numeric giving the default length of links in pixels used in the app. The user can change this interactively in the app.

launch_browser

logical, if TRUE, the application is opened in the system's default browser, if FALSE, no browser is started. If the argument is omitted, the value according to the option shiny.launch.browser is used, which in RStudio opens the internal shiny viewer.