R/mod_displayTree.R

In jennahamlin/annoatater: An Amazing Shiny App

#' displayTree UI Function
#'
#' @description A shiny Module.
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#'
#' @noRd 
#'
#' @importFrom shiny NS tagList 
mod_displayTree_ui <- function(id){
  ns <- NS(id)
  tagList(
 
  )
}
    
#' displayTree Server Function
#'
#' @noRd 
mod_displayTree_server <- function(input, output, session,
                                   treeFileOut, geneFileCorOrUnOut, treeformat, lim, align, font, numscale, node, midP){
  ns <- session$ns
  
  #convert phylogenetic tree (midpoint or not) to tibble to join tree and genetic distance matrix
  treeObject<-reactive({
    tibble::as_tibble(treeFileOut())
  })
  
  #change column1, row1 to the id of label and replace - with a 0 within the file
  geneObject <- reactive({
    label <- . <- NULL
    dplyr::rename(geneFileCorOrUnOut(), label = 1)%>%
      replace(., .=="-", 0)
  })
  
  #join the treeobject and updated genetic distance file by label and convert to s4 object
  gandTS4 <- reactive({
    dplyr::full_join(treeObject(), geneObject(), by = "label")%>%
      treeio::as.treedata()
  })
  
  treePlot <- function(inputFile){
    ggtree::ggtree(inputFile, layout = treeformat())+
      ggplot2::xlim(NA, lim())+
      ggtree::geom_tiplab(align = align(), fontface = font(), family="Helvetica")
  }

  # treePlot <- reactive( {
  #     ggtree::ggtree(treeFileOut(), layout = treeformat())+
  #       ggplot2::xlim(NA, lim())+
  #       ggtree::geom_tiplab(align = align(), fontface = font(), family="Helvetica") +
  #       ggtree::geom_treescale(width = numscale())+
  #       ggtree::geom_text2(ggplot2::aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > node()), nudge_x = 0.00025)
  #   })
  
  #major plotting reactive using an S4 object called above (gandTS4) or the base midTree reactive made from import of treeFileOut and the  Upload data module
  makeTree <- reactive({treePlot(treeFileOut())})

  return(
    list(
      makeTreeOut = reactive(makeTree())
    ))

  

  
  # ## displayTree server functions
  # treePlot <- function(inputFile){
  #   ggtree::ggtree(inputFile, layout = treeformat())+
  #     ggplot2::xlim(NA, lim())+
  #     ggtree::geom_tiplab(align = align(), fontface = font(), family="Helvetica") +
  #     ggtree::geom_treescale(width = numscale())+
  #     ggtree::geom_text2(ggplot2::aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > node()), nudge_x = 0.00025)
  # 
  # }
  # 
  # midTree <- reactive({
  #   if(midP() == TRUE) {
  #     return(phytools::midpoint.root(treeFileOut()))
  #   }
  #   else {
  #     return(treeFileOut())
  #   }
  # })
  # 
  # #major plotting reactive using an S4 object called above (gandTS4) or the base midTree reactive made from import of treeFileOut and the  Upload data module
  # makeTree <- reactive({
  #   
  #   treePlot(treeFileOut())
  # 
  #   # if(midP((input$id)){ # this disconnects the need for genetic distance file to be uploaded.
  #   #   treePlot(midTree())
  #   # }
  #   # else{
  #   #   treePlot(gandTS4())
  #   # }
  # })
  # 
  # #return these reactive objects to be used in cladeAnnotator module
  # return(
  #   list(
  #     geneObjectOut = reactive(geneObject()),
  #     makeTreeOut = reactive(makeTree())
  #   ))
}
    
## To be copied in the UI
# mod_displayTree_ui("displayTree_ui_1")
    
## To be copied in the server
# callModule(mod_displayTree_server, "displayTree_ui_1")