Shiny outer module to integrate draw and annotation inner modules

Shiny outer module to integrate draw and annotation inner modules

main_server(id, phylogeny, draw_modules, anno_module = FALSE)

main_ui(id, phylogeny, draw_modules, anno_module = FALSE)

Arguments

id	character, namespace id
phylogeny	object of class phylo to draw
draw_modules	character. Modules to include in the tree-drawing application (or page). The modules are specified through their Initial as given in show_modules(). See ?show_modules for available options.
anno_module	logical. Whether to include the 'clade_annotation' module (annotate_ui/server)

Value

UI and server logic for plotting and interactive modification of a phylogeny

Details

Trees with > 200 tips will in most cases be illegible. Tip names become illegible in smaller trees.

Examples

if (interactive()) {
  library(shiny)
  library(phynotate)
  library(ape)

  ui <- shiny::navbarPage(
    title = "A shiny app where we need to include a page for phylogeny viz",
    tabPanel(title = "Download sequences"),
    tabPanel(title = "Infer orthology"),
    tabPanel(
      title = "Vizualize and download trees",
      phynotate::main_ui(
        id = "id",
        draw_modules = "LPTB",
        anno_module = FALSE
      )
    )
  )

  server <- function(input, output, session) {
    # Server code to download sequences
    # Server code to infer orthology

    # Send a user selected tree to the phynotate viz module
    main_server(id = "id",
                phylogeny = ape::rcoal(20),
                #phylogeny = input[["user_selected_tree"]],
                draw_modules = "LPTB")
  }

  shinyApp(ui = ui, server = server)
}