command line script to launch a QT app in SafetyGraphics V2 framework

sg_QT_cmd.R

# QT Shiny modules
# https://github.com/SafetyGraphics/safetyGraphics/wiki/ChartConfiguration#example-2---static-outlier-explorer
# Use sample clinical trial data sets from the {safetyData} package
library(safetyData)
library(safetyGraphics)
library(ggplot2)
library(dplyr)
library(yaml)
library(plotly)
library(forcats)


# Sample ADEG data
# https://physionet.org/content/ecgcipa/1.0.0/
# https://physionet.org/content/ecgcipa/1.0.0/adeg.csv

adeg <- readr::read_csv("https://physionet.org/files/ecgcipa/1.0.0/adeg.csv?download") %>%
  mutate(ATPTFCT = forcats::fct_reorder(ATPT, .x = ATPTN, .fun = min)) %>%
  mutate(ANRHI=0, ANRLO=0)


# QT module

safetyOutlierExplorerQT_ui <- function(id) {
  ns <- NS(id)
  sidebar<-sidebarPanel(
    uiOutput(ns("selectMeasures"))
  )
  main<-mainPanel(
    tabsetPanel(
      tabPanel("QT Data Info", verbatimTextOutput(ns("info"))),
      tabPanel("QT Vis", plotlyOutput(ns("outlierExplorerQT"), height = 800))
    )

  )
  ui<-fluidPage(
    sidebarLayout(
      sidebar,
      main,
      position = c("right"),
      fluid=TRUE
    )
  )
  return(ui)
}


safety_outlier_explorerQT <- function(data, settings)
{

  # rich graph

  hline <- function(y = 0, color = "blue") {
    list(
      type = "line",
      x0 = 0,
      x1 = 1,
      xref = "paper",
      y0 = y,
      y1 = y,
      line = list(color = color, width= 2, dash = 'dash')
    )
  }



  (
    fig <- data %>%
      filter(!!sym(settings$measure_col) %in% settings$measure_values)  %>%
      mutate(Y450 = 450-BASE, Y480=480-BASE, Y500=500-BASE) %>%
      plot_ly(
        x = ~BASE,
        y = ~CHG,
        size = ~CHG,
        color = ~TRTA,
        frame = ~paste0(sprintf("%02d", ATPTN), " - ", ATPT),
        text = ~paste0(PARAM, "<br>Time point: ", ATPT, "<br>Treatment: ",
                       TRTA, "<br>Baseline:", BASE, "<br>Change: ", CHG),
        hoverinfo = "text",
        type = 'scatter',
        mode = 'markers'
      ) %>%
      animation_slider(
        currentvalue = list(prefix = "Time Point: ")
      )

  )

  fig  %>%
    layout(shapes = list(hline(0), hline(30), hline(60),
                         list(type="line", width= 2,  line = list(dash = 'dash',color = "red"),
                              x0=0, x1=450, y0=450, y1=0)))


}

safetyOutlierExplorerQT_server <- function(input, output, session, params) {

  #browser()

  ns <- session$ns


  output$selectMeasures <- renderUI({
    measure_col <- params()$settings$measure_col
    measures <- unique(params()$data[[measure_col]])


    selectizeInput(
      ns("measures"),
      "Select Measures",
      multiple=TRUE,
      choices=measures,
      selected = "QTcF"
    )
  })

  # Populate control with measures and select all by default

  # customize selected measures based on input
  settingsR <- reactive({
    settings <- params()$settings
    settings$measure_values <- input$measures
    return(settings)
  })

  # data info

  output$info <- renderPrint({

    params()$data %>% count(APERIOD, ATPTFCT, sort=FALSE) %>% data.frame

  })

  #draw the chart
  output$outlierExplorerQT <- renderPlotly({
    req(input$measures)
    safety_outlier_explorerQT(params()$data, settingsR())
  })
}


outlierQTMod_yaml <- '
env: safetyGraphics
label: QT Outlier Explorer - Module
type: module
package: safetyCharts
domain:
  - labs
workflow:
  ui: safetyOutlierExplorerQT_ui
  server: safetyOutlierExplorerQT_server
links:
  safetyCharts: https://github.com/SafetyGraphics/safetycharts
'



QTcharts <- makeChartConfig() %>% purrr::keep(~(max(.x$domain == "labs")>0))
QTcharts$outlierQTMod<-prepareChart(read_yaml(text=outlierQTMod_yaml))

mappings_QT <- read_yaml(text=
                           "
labs:
  id_col: USUBJID
  value_col: AVAL
  measure_col: PARAM
  measure_values:
    ALT: ''
    AST: ''
    TB: ''
    ALP: ''
  normal_col_low: ANRLO
  normal_col_high: ANRHI
  studyday_col: ADY
  visit_col: ATPT
  visitn_col: ATPTN
  unit_col: EGSTRESU
  baseline_flag_col: ABLFL
  baseline_flag_values: 'Y'
  analysis_flag_col: ''
  analysis_flag_values: ''
")

safetyGraphicsApp(charts=QTcharts, domainData = list(labs=adeg), mapping = mappings_QT)