inst/gghisse-web/gghisse/modules/module_h_scatterplot.R

In teofiln/utilhisse: A Collection of Functions for Summarising and Visualizing 'hisse' Results

params <- c(
  "Net turnover",
  "Extinction fraction",
  "Speciation",
  "Extinction",
  "Net diversification"
)

theme_h_scatter <- theme_classic() +
  theme(axis.text = element_text(size = 12),
        axis.title = element_text(size = 14),
        plot.background = element_rect(color="black", size = 1))

##### --- h_scatterplot ui  ---------------------- #####

h_scatterplot_ui <- function(id) {
  ns <- NS(id)
  tagList(
    checkboxGroupButtons(
      inputId = ns("h_scatter"),
      choiceNames = "Scatterplot of model averaged diversification rates",
      choiceValues = 1,
      status = "primary",
      selected = "Scatterplot of model averaged diversification rates"
    ),
    
    conditionalPanel(
      condition = paste0("input['", ns("h_scatter"), "'] == 1"),
      wellPanel(fluidRow(
      column(
        3,
        # parameter
        selectInput(
          inputId = ns("parameter"),
          label = "Parameter:",
          choices = params,
          selected = "Net turnover"
        ),
        # states_names
        textInput(
          inputId = ns("states_names1"),
          label = "State 0:",
          placeholder = "Character state 0",
          value = 0
        ),
        textInput(
          inputId = ns("states_names2"),
          label = "State 1:",
          placeholder = "Character state 1",
          value = 1
        ),
        # plot_as_waiting_time
        checkboxInput(
          inputId = ns("plot_as_waiting_time"),
          label = "Plot as waiting time",
          value = FALSE
        ),
        actionButton(inputId = ns("plot"), label = "Plot"),
        actionButton(inputId = ns("code"), label = "Code")
      ),
      column(width = 4, 
             plotOutput(ns("plt")),
             tags$hr(),
             uiOutput(ns("plt_txt"), container = tags$code)
             )
    )
  )))
}

##### --- h_scatterplot srv ---------------------- #####

h_scatterplot_srv <-
  function(input,
           output,
           session,
           h_obj) {
    h_proc <- reactive({
      x <- h_process_recon(h_obj ())
      return(x)
    })
    
    param <- reactive({
      x <- case_when(
        input$parameter == "Net turnover" ~ "turnover",
        input$parameter == "Extinction fraction" ~ "extinct.frac",
        input$parameter == "Speciation" ~ "speciation",
        input$parameter == "Extinction" ~ "extinction",
        input$parameter == "Net diversification" ~ "net.div"
      )
      return(x)
    })
    
    plt <- eventReactive(input$plot, {
      p <- h_scatterplot(
        processed_recon = h_proc(),
        parameter = param(),
        states_names = c(input$states_names1, input$states_names2),
        colors = c("firebrick", "steelblue"),
        plot_as_waiting_time = input$plot_as_waiting_time
      ) +
        theme_h_scatter
      return(p)
    })
    
    output$plt <- renderPlot({
      plt()
    })
    
    plt_txt <- eventReactive(input$code, {
      
      code_text <- paste("<b>Code to reproduce this figure in an R session: </b><br/>",
                         "<br/>",
                         "library(hisse)",
                         "<br/>library(utilhisse) # will load other dependencies",
                         "<br/>h_proc <- h_process_recon(your_hisse_recon_object)",
                         "<br/>h_scatterplot(",
                         "<br/>&nbsp;&nbsp;&nbsp;&nbsp;processed_recon = h_proc,",
                         "<br/>&nbsp;&nbsp;&nbsp;&nbsp;parameter = '", c(param()),"',",
                         "<br/>&nbsp;&nbsp;&nbsp;&nbsp;states_names = c(", input$states_names1, ",", input$states_names2, "),",
                         "<br/>&nbsp;&nbsp;&nbsp;&nbsp;colors = c('firebrick', 'steelblue')", ",",
                         "<br/>&nbsp;&nbsp;&nbsp;&nbsp;plot_as_waiting_time = ", input$plot_as_waiting_time,
                         "<br/>) + theme_classic()",
                         "<br/>",
                         "<br/># For more information see ?utilhisse::h_scatterplot", sep="")
      p <-
        wellPanel(
          class = "code_well",
          tags$style(".code_well {background-color: white ;}"),
          HTML(code_text)
        )
      return(p)
    })
    
    output$plt_txt <- renderUI({
      plt_txt()
    })
    
  }