Problem with shiny app creation and output in R

Question

I'm very new in creating a shiny app. Need some help in resolving the errors. So, I have some data like below in file final.csv:

structure(list(Samples = structure(c(1L, 12L, 23L, 34L, 45L, 
46L, 47L, 48L, 49L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 
13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 24L, 25L, 26L, 
27L, 28L, 29L, 30L, 31L, 32L, 33L, 35L, 36L, 37L, 38L, 39L, 40L, 
41L, 42L, 43L, 44L), .Label = c("Sample1", "Sample10", "Sample11", 
"Sample12", "Sample13", "Sample14", "Sample15", "Sample16", "Sample17", 
"Sample18", "Sample19", "Sample2", "Sample20", "Sample21", "Sample22", 
"Sample23", "Sample24", "Sample25", "Sample26", "Sample27", "Sample28", 
"Sample29", "Sample3", "Sample30", "Sample31", "Sample32", "Sample33", 
"Sample34", "Sample35", "Sample36", "Sample37", "Sample38", "Sample39", 
"Sample4", "Sample40", "Sample41", "Sample42", "Sample43", "Sample44", 
"Sample45", "Sample46", "Sample47", "Sample48", "Sample49", "Sample5", 
"Sample6", "Sample7", "Sample8", "Sample9"), class = "factor"), 
    years = c(1.301369863, 0.4, 1.054794521, 0.134246575, 0.794520548, 
    3.287671233, 3.646575342, 3.887671233, 3.646575342, 3.619178082, 
    3.575342466, 2.02739726, 3.523287671, 3.742465753, 2.926027397, 
    3.8, 1.161643836, 1.380821918, 3.087671233, 3.104109589, 
    3.084931507, 2.887671233, 2.778082192, 2.728767123, 3.043835616, 
    1.210958904, 2.704109589, 2.742465753, 2.635616438, 2.536986301, 
    2.432876712, 2.794520548, 1.967123288, 1.84109589, 1.838356164, 
    2.726027397, 2.430136986, 2.257534247, 1.876712329, 2.010958904, 
    0.698630137, 2.090410959, 2.098630137, 2.01369863, 1.717808219, 
    1.81369863, 2.057534247, 2.032876712, 1.989041096), patient.vital_status = c(0L, 
    0L, 0L, 1L, 1L, 0L, 1L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 
    1L, 1L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L), A1BG = structure(c(1L, 1L, 2L, 2L, 1L, 2L, 2L, 
    1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 
    2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 
    1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L), .Label = c("high", 
    "low"), class = "factor"), A1CF = structure(c(1L, 1L, 1L, 
    1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 
    2L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    2L), .Label = c("high", "low"), class = "factor")), class = "data.frame", row.names = c(NA, 
-49L))

Using the above information I'm trying to create an app, but having some trouble to make it correct. Below is the code I used:

library(shiny)
library(shinyjs)
library(tidyverse)
library(survminer)

ui <- fluidPage(
  titlePanel("survival"),
  sidebarLayout(
    sidebarPanel(
      selectInput(inputId = "thegene", label = "Gene", choices = c("A1BG", "A1CF"), selected = "A1CF"),
      radioButtons(inputId = "FileType", label = "Select the file type", choices = list("png", "pdf"), selected = "pdf"),
      width = 3
    ),
    mainPanel(
      plotOutput("plot"),
      downloadButton(outputId = "downloadPlot", label = "Download the plot"),
      width = 9
    )
  )
)

server <- function(input, output, session) {
  final <- read.csv("final.csv")
  genes <- as.factor(names(final[c(4:5)]))

  vals <- reactiveValues()

  alldat <- reactive({
    choices <- genes
    selected <- isolate(input$thegene)
    if (!selected %in% choices) selected <- choices[1]
    updateSelectInput(session, "thegene", choices = choices, selected = selected)
    final
  })

  dat <- reactive({
    x <- alldat()
    x[ x$variable == input$thegene,,drop=FALSE]
  })

  output$plot <- renderPlot({
      fit <- survfit(as.formula(paste0("Surv(years, patient.vital_status) ~", names(final[c(4:5)]))),
                     data = final)
      gg <-ggsurvplot(fit,
                 pval = TRUE, conf.int = FALSE,
                 risk.table = TRUE, # Add risk table
                 risk.table.col = "strata", # Change risk table color by groups
                 linetype = "strata", # Change line type by groups
                 surv.median.line = "hv", # Specify median survival
                 ggtheme = theme_bw(), # Change ggplot2 theme
                 palette = c("#FF0027", "#060606"),
                 xlim = c(0,10),
                 break.x.by = 3,
                 xlab="Time in years",
                 risk.table.y.text.col = T, # colour risk table text annotations.
                 risk.table.y.text = FALSE)
    vals$gg <- gg
    print(gg)
  })

  output$downloadPlot <- downloadHandler(
    filename =  function() {
      paste(input$thegene, input$FileType,sep=".")
    },
    # content is a function with argument file. content writes the plot to the device
    content = function(file){
      if(input$FileType=="png")
        png(file, units="in", width=5, height=5, res=300)
      else
        pdf(file, width = 5, height = 5, onefile = FALSE)
      print(vals$gg)
      dev.off()
    } 
  )
}

# Run the application 
shinyApp(ui = ui, server = server)

With the above code when I run the app, I have an error.

Error: object 'final' not found

As I see the above ERROR, so before running the app I loaded the final.csv and also assigned the column names of 4th and 5th column to genes myself. And then when I run the app looks like it worked but, I could see only A1BG gene output. When I selected A1CF gene in the interface, I don't see that output instead I see again A1BG output.

Answer 1

The reason the plot isn't updating is because you are using names(final[c(4:5)])) as the predictor variable in survfit, whereas I think you are wanting to use input$thegene instead. Seems to work as intended that way.

Couple of other suggestions/notes:

• You can probably get away with changing alldat into an observe and just calling final in the dat reactive as you aren't manipulating it in any way in the first reactive.
• There seem some other issues with the app (such as the survival package not explicitly loaded and "variable" not existing in final names). Might be worth having a look at these too.

Answer 2

The problem comes from the if condition in alldata: you have to replace if(!selected %in% choices) by if (choices != NULL) since choices will be NULL only if the dataframe final does not exist (i.e is not imported).

You now have some trouble with functions in the survminer package but that's another problem and surely it comes from some typo in functions.