Error in rep: attempt to replicate an object of type 'closure' (Boxplots in if statements)

0
votes

I have a code that is supposed to make a boxplot maker. It is very close to working (thanks to a bunch of people on this website). The problem that I have now is that whenever I run the code, I get the Error in rep: attempt to replicate an object of type 'closure' warning. The stack trace shows that it comes directly from the line of code that makes the boxplot (whichever one runs). Is the problem that I cannot have a boxplot inside of an if statement? I feel like that isn't true. Any help you can offer would be greatly appreciated. Here's the code:

library(shiny)
All_Data <- data.frame(
    Name = as.character(c("Jeff","Bob","Greg")),
    Year = c(2015,2015,2015),
    Bacteria = c("A","B","C"),
    Site = c("C1","C1","C1"),
    Percents = c(1,2,4),
stringsasfactors = TRUE
)
ndata <-data.frame(
    Name = as.character("Preset"),
    Year = c("0"),
    Bacteria = as.factor(c("0")),
    Site = as.factor(c("0")),
    Percents = as.numeric(c("0")),
    stringsAsFactors = TRUE
)
Names <- c("Jeff", "Bob", "Greg")
Years <- c("0")
names(Years)<-c("2015 C2")
Sites <- c("","C1")
# Define UI for application
ui <- fluidPage(
    
    # Application title
    titlePanel("ISAMR DNA Group Boxplot Maker"),
    
    # Sidebar
    sidebarLayout(
        sidebarPanel(width = 4,
                     h3("Which Data Sets Would You Like to Compare?"),
                     selectInput("Set1", "", choices = c(Sites, Years, Names)),
                     selectInput("Set2", "",choices = c(Sites, Years, Names)),
                     selectInput("factor","Based on Which Factor?", choices = c("Year", "Site", "Bacteria", "Site by Year", "Bacteria by Year", "Bacteria by Site by Year")),
                     textInput("title", h4("Title"), placeholder = "Enter title..."),
                     numericInput("numcol","How many colors?",value=1,min=1,max=5),
                     h4("Pick the colors you want, leave the rest blank."),
                     selectInput("col1","",choices = c("",colors())),
                     selectInput("col2","",choices = c("",colors())),
                     selectInput("col3","",choices = c("",colors())),
                     selectInput("col4","",choices = c("",colors())),
                     selectInput("col5","",choices = c("",colors())),
                     actionButton("Submit", "Submit")
        ),
        
        # Show a chosen plot
        mainPanel(
            #uiOutput("data"),
            DT::dataTableOutput("data"),
            plotOutput("plot")
        )
    )
)

# Define server logic
server <- function(input, output) {
    
    createframe<-eventReactive(input$Submit, {req(input$Submit)
        
        if (input$Set1 %in% Names & input$Set2 %in% Names){
            ndata <- filter(All_Data, All_Data$Name == input$Set1 | All_Data$Name == input$Set2)
        }
        else if (input$Set1 %in% Names & input$Set1 %in% Years){
            ndata <- filter(All_Data, All_Data$Name == input$Set1 | All_Data$Year == input$Set2)
        }
        else if (input$Set1 %in% Names & input$Set1 %in% Sites){
            ndata <- filter(All_Data, All_Data$Name == input$Set1 | All_Data$Site == input$Set2)
        }
        else if (input$Set1 %in% Years & input$Set1 %in% Names){
            ndata <- filter(All_Data, All_Data$Site == input$Set1 | All_Data$Name == input$Set2)
        }
        else if (input$Set1 %in% Years & input$Set2 %in% Years){
            ndata <- filter(All_Data, All_Data$Year == input$Set1 | All_Data$Year == input$Set2)
        }
        else if (input$Set1 %in% Years & input$Set2 %in% Sites){
            ndata <- filter(All_Data, All_Data$Year == input$Set1 | All_Data$Site == input$Set2)
        }
        else if (input$Set1 %in% Sites & input$Set1 %in% Names){
            ndata <- filter(All_Data, All_Data$Site == input$Set1 | All_Data$Name == input$Set2)
        }
        else if (input$Set1 %in% Sites & input$Set1 %in% Years){
            ndata <- filter(All_Data, All_Data$Site == input$Set1 | All_Data$Year == input$Set2)
        }
        else if (input$Set1 %in% Sites & input$Set1 %in% Sites){
            ndata <- filter(All_Data, All_Data$Site == input$Set1 | All_Data$Site == input$Set2)
        }   })
    
    output$data <- DT::renderDataTable({
        createframe()
    })
    observeEvent(input$numcol,{req(input$numcol)
        if (input$numcol == 1){coll<-c(input$col1)}
        if (input$numcol == 2){coll<-c(input$col1,input$col2)}
        if (input$numcol == 3){coll<-c(input$col1,input$col2,input$col13)}
        if (input$numcol == 4){coll<-c(input$col1,input$col2,input$col3,input$col4)}
        if (input$numcol == 5){coll<-c(input$col1,input$col2,input$col3,input$col4,input$col5)}
    })    
    
    observeEvent(input$factor,{req(input$factor)
        output$plot <- renderPlot(
        if (input$factor == "Year"){
                boxplot(Percents ~ Year, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)
        }
        
        else if (input$factor == "Site"){
                boxplot(Percents ~ Site, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)   
        }
        
        else if (input$factor == "Bacteria"){
                boxplot(Percents ~ Bacteria, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)
        }
        
        else if (input$factor == "Site by Year"){
                boxplot(Percents ~ Year%in%Site, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)
        }
        
        else if (input$factor == "Bacteria by Year"){
                boxplot(Percents ~ Year%in%Bacteria, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)
        }
        
        else if (input$factor == "Bacteria by Site by Year"){
                boxplot(Percents ~ Year%in%Site%in%Bacteria, data = ndata, main = input$title, ylab = "Relative Abundance", col = coll)
        }
    )})
}

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

(Not the real data)

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggrepel_0.8.2   ggthemes_4.2.0  shiny_1.5.0     dslabs_0.7.3    forcats_0.5.0   stringr_1.4.0   dplyr_1.0.0     purrr_0.3.4     readr_1.3.1    
[10] tidyr_1.1.0     tibble_3.0.3    ggplot2_3.3.2   tidyverse_1.3.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        lubridate_1.7.9   assertthat_0.2.1  digest_0.6.25     mime_0.9          R6_2.4.1          cellranger_1.1.0  backports_1.1.7  
 [9] reprex_0.3.0      httr_1.4.1        pillar_1.4.6      rlang_0.4.7       readxl_1.3.1      rstudioapi_0.11   blob_1.2.1        DT_0.14          
[17] labeling_0.3      htmlwidgets_1.5.1 munsell_0.5.0     tinytex_0.24      broom_0.7.0       compiler_4.0.2    httpuv_1.5.4      modelr_0.1.8     
[25] xfun_0.15         pkgconfig_2.0.3   htmltools_0.5.0   sourcetools_0.1.7 tidyselect_1.1.0  fansi_0.4.1       crayon_1.3.4      dbplyr_1.4.4     
[33] withr_2.2.0       later_1.1.0.1     grid_4.0.2        jsonlite_1.7.0    xtable_1.8-4      gtable_0.3.0      lifecycle_0.2.0   DBI_1.1.0        
[41] magrittr_1.5      scales_1.1.1      cli_2.0.2         stringi_1.4.6     farver_2.0.3      fs_1.4.2          promises_1.1.1    xml2_1.3.2       
[49] ellipsis_0.3.1    generics_0.0.2    vctrs_0.3.2       tools_4.0.2       glue_1.4.1        hms_0.5.3         crosstalk_1.1.0.1 rsconnect_0.8.16 
[57] fastmap_1.0.1     yaml_2.2.1        colorspace_1.4-1  rvest_0.3.5       haven_2.3.1

Stack Trace:

Warning: Error in rep: attempt to replicate an object of type 'closure'
  174: pcycle
  173: bxp
  171: boxplot.default
  169: boxplot.formula
  167: renderPlot [C:\Users\pferr\Desktop\Test/app.R#102]
  165: func
  125: drawPlot
  111: <reactive:plotObj>
   95: drawReactive
   82: origRenderFunc
   81: output$plot
    1: runApp
1
rshinyboxplotshiny-reactivity
The error usually means that you are treating a function as if it was an object. Looking at your code I'm not clear on where it's occurring, but it may go away if you remove the observeEvent() for the boxpot and instead store the boxplot object into a eventReactive() object, and then run renderPlot() outside of that. – Phil
Also, Year%in%Site%in%Bacteria doesn't make any sense. – Phil
stringsasfactors = TRUE is wrong, should be stringsAsFactors = TRUE – r2evans
You should not be using & in an if statement: the former suggests "0 or more logicals", whereas the latter requires always length 1. It will generally work alright here, but (1) it is bad programming practice, and more important (2) it does not support logical short-circuiting (see FALSE && stop("oops") vs FALSE & stop("oops")). Same for | vs ||. – r2evans
Frankly, SamFerraro, there are so many basic R problems here with the code that I suggest you try to get this to work on the console before trying to make it work in shiny. Realize that ndata <- ... inside of a reactive/observe block is not necessarily going to update the ndata you define in the globals, so ... there is a lot of restructuring you need to do with this to get it to behave. – r2evans

1 Answers

0
votes

You had a couple of issues. First, color definition was an issue. A missing choice was also causing issue. So, I made it a reactive. Second, you were using ndata as data in the boxplots. Once you fix them, it works fine. Please see the code below.

library(shiny)

ndata <-data.frame(
  Name = as.character("Preset"),
  Year = c("0"),
  Bacteria = as.factor(c("0")),
  Site = as.factor(c("0")),
  Percents = as.numeric(c("0")),
  stringsAsFactors = TRUE
)
Names <- c("Jeff", "Bob", "Greg")
Years <- c("0")
names(Years)<-c("2015 C2")
Sites <- c("","C1")
# Define UI for application
ui <- fluidPage(

  # Application title
  titlePanel("ISAMR DNA Group Boxplot Maker"),

  # Sidebar
  sidebarLayout(
    sidebarPanel(width = 4,
                 h3("Which Data Sets Would You Like to Compare?"),
                 selectInput("Set1", "", choices = c(Sites, Years, Names)),
                 selectInput("Set2", "",choices = c(Sites, Years, Names)),
                 selectInput("factor","Based on Which Factor?", 
                             choices = c("Year", "Site", "Bacteria", "Site by Year", "Bacteria by Year", "Bacteria by Site by Year")),
                 textInput("title", h4("Title"), placeholder = "Enter title..."),
                 numericInput("numcol","How many colors?",value=1,min=1,max=5),
                 h4("Pick the colors you want, leave the rest blank."),
                 selectInput("col1","",choices = c(colors())),
                 selectInput("col2","",choices = c(colors())),
                 selectInput("col3","",choices = c(colors())),
                 selectInput("col4","",choices = c(colors())),
                 selectInput("col5","",choices = c(colors())),
                 actionButton("Submit", "Submit")
    ),

    # Show a chosen plot
    mainPanel(
      #uiOutput("data"),
      DT::dataTableOutput("data")
      ,plotOutput("plot")
    )
  )
)

# Define server logic
server <- function(input, output) {

  All_Data <- data.frame(
    Name = as.character(c("Jeff","Bob","Greg")),
    Year = c(2015,2015,2015),
    Bacteria = c("A","B","C"),
    Site = c("C1","C1","C1"),
    Percents = c(1,2,4),
    stringsAsFactors = TRUE
  )
  
  dframe<-reactive({
    req(input$Set1,input$Set2)

    if (input$Set1 %in% Names & input$Set2 %in% Names){
      ndata <- filter(All_Data, All_Data$Name %in% input$Set1 | All_Data$Name %in% input$Set2)
    }
    else if (input$Set1 %in% Names & input$Set2 %in% Years){
      ndata <- filter(All_Data, All_Data$Name %in% input$Set1 | All_Data$Year %in% input$Set2)
    }
    else if (input$Set1 %in% Names & input$Set2 %in% Sites){
      ndata <- filter(All_Data, All_Data$Name %in% input$Set1 | All_Data$Site %in% input$Set2)
    }
    else if (input$Set1 %in% Years & input$Set2 %in% Names){
      ndata <- filter(All_Data, All_Data$Site %in% input$Set1 | All_Data$Name %in% input$Set2)
    }
    else if (input$Set1 %in% Years & input$Set2 %in% Years){
      ndata <- filter(All_Data, All_Data$Year %in% input$Set1 | All_Data$Year %in% input$Set2)
    }
    else if (input$Set1 %in% Years & input$Set2 %in% Sites){
      ndata <- filter(All_Data, All_Data$Year %in% input$Set1 | All_Data$Site %in% input$Set2)
    }
    else if (input$Set1 %in% Sites & input$Set2 %in% Names){
      ndata <- filter(All_Data, All_Data$Site %in% input$Set1 | All_Data$Name %in% input$Set2)
    }
    else if (input$Set1 %in% Sites & input$Set2 %in% Years){
      ndata <- filter(All_Data, All_Data$Site %in% input$Set1 | All_Data$Year %in% input$Set2)
    }
    else if (input$Set1 %in% Sites & input$Set2 %in% Sites){
      ndata <- filter(All_Data, All_Data$Site %in% input$Set1 | All_Data$Site %in% input$Set2)
    }else{ndata <- NULL}
    return(ndata)
  })

  output$data <- DT::renderDataTable({
    dframe()
  })

  coll <- reactive({
    req(input$numcol)
    if   (is.null(input$numcol)) {coll <- c("red")
    }else if (input$numcol == 1) {coll <- c(input$col1)
    }else if (input$numcol == 2) {coll <- c(input$col1,input$col2)
    }else if (input$numcol == 3) {coll <- c(input$col1,input$col2,input$col13)
    }else if (input$numcol == 4) {coll <- c(input$col1,input$col2,input$col3,input$col4)
    }else if (input$numcol == 5) {coll <- c(input$col1,input$col2,input$col3,input$col4,input$col5)
    }else                        {coll <- c("orange")}
    coll
  })

  observeEvent(input$Submit, {

    req(input$factor,input$Submit)
    if (is.null(input$factor) | input$Submit==0){
      return(NULL)
    }else{

      output$plot <- renderPlot({

        if (input$factor == "Year"){
          boxplot(Percents ~ Year, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else if (input$factor == "Site"){
          boxplot(Percents ~ Site, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else if (input$factor == "Bacteria"){
          boxplot(Percents ~ Bacteria, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else if (input$factor == "Site by Year"){
          boxplot(Percents ~ Year%in%Site, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else if (input$factor == "Bacteria by Year"){
          boxplot(Percents ~ Year%in%Bacteria, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else if (input$factor == "Bacteria by Site by Year"){
          boxplot(Percents ~ Year%in%Site%in%Bacteria, data = dframe(), main = input$title, ylab = "Relative Abundance", col = coll())
        }else {return(NULL)}
      })

    }
  })

}

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

output