Automatic sleep stage scoring shiny 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)