Automatic sleep stage scoring shiny app

Source code of the shiny app at https://shiny.analysed.ch/scoring_app/

library(shiny)
library(shinydashboard)
library(plotly)
library(dplyr)

# Load spectra
spectra <- vroom::vroom('spectra.txt')
# stages 
stages <- vroom::vroom('stages.txt')
# signal
signal <- vroom::vroom('signal.txt')

ui <- dashboardPage(
  dashboardHeader(title = 'Scoring app'),
  dashboardSidebar(
    sidebarMenu(
      menuItem("Sleep EEG", tabName = "spe_tra", icon = icon("procedures"))
    )
  ),
  dashboardBody(
    tabItems(
      tabItem("spe_tra",
              box(plotlyOutput("eeg_plot"), width = 11),
              box(numericInput("Epoch_sl", "Select Epoch:", 1, min = 1, max = 1282), width = 1, 
                  tags$a(href="https://blog.analysed.ch/books/analysedch-apps/page/automatic-sleep-stage-scoring-shiny-app", "Source code of this app")),
              box(plotlyOutput("plot_old"), width = 10),
              box(plotlyOutput("plot_spec"), width = 2)
      )
    )
  )
)

server <- function(input, output){

  output$eeg_plot <- renderPlotly({
    ggplotly(ggplot(signal %>% dplyr::filter(Epoch == input$Epoch_sl), mapping = aes(x = time, Amplitude)) + 
               geom_line()+ facet_wrap(vars(Channel),nrow = 4)+ geom_hline(yintercept = 0,  alpha = 0.3)+
               geom_hline(yintercept = c(-75,75), lty = 7, alpha = 0.3)+
               labs(x = 'Time (h)', y = 'uV') + 
               scale_colour_viridis_d(begin = 0.1, end = 0.7) + theme_classic())
  })
  output$plot_old <- renderPlotly({
    
    fig <- plot_ly(spectra, x = ~Epoch, y = ~Freq, z = ~Power, colors = "Spectral") %>%  
      add_heatmap() %>% colorbar(title = "-Log\nPower")
    
    fig1 <- plot_ly(stages, x = ~Epoch, name = 'Manually\nscored') %>% 
      add_ribbons(ymin = ~man_scored - 0.5, ymax = ~man_scored + 0.5, color= I("black")) %>%
      add_segments(x = input$Epoch_sl, xend = input$Epoch_sl, y = -1.5, yend = 3.5, showlegend = FALSE, color=I('red'))  %>%
      plotly::layout(
        yaxis = list(
          range=c(-1.5,4),
          ticktext = list("REM", "Wake", "N1", "N2", "SWS"),
          tickvals = list(-1, 0, 1, 2, 3),
          tickmode = "array"
        ))
    
    fig2 <- plot_ly(stages, x = ~Epoch, name = 'Autom.\nscored') %>%
      add_ribbons(ymin = ~Stages - 0.5, ymax = ~Stages + 0.5, color = I("blue")) %>%
      add_segments(x = input$Epoch_sl, xend = input$Epoch_sl, y = -1.5, yend = 3.5, showlegend = FALSE, color=I('red'))  %>%
      plotly::layout(
        yaxis = list(
          range=c(-1.5,4),
          ticktext = list("REM", "Wake", "N1", "N2", "SWS"),
          tickvals = list(-1, 0, 1, 2, 3),
          tickmode = "array"
        )
      )
    subplot(fig, fig1, fig2 , nrows = 3)
  })
  
  output$plot_spec <- renderPlotly({
    ggplotly(ggplot(spectra %>% dplyr::filter(Epoch == input$Epoch_sl), mapping = aes(x = Freq, y=-Power)) + 
               geom_line() + labs(x = 'Frequency', y = 'Power', title='PSD in epoch\nof interest') + 
               scale_colour_viridis_d(begin = 0.1, end = 0.7) + theme_classic() + theme(plot.title = element_text(hjust = 0.5)))
  })
}

shinyApp(ui, server)