printing a output of a variable in shiny

shiny
1

Dear All,
I was wondering if someone could please help me? I am new to working in Shiny apps using Rstudio. I am facing an issue with the coding, I am printing a ggplot by uploading a CSV file which works fine. Issue I am facing is to print values of certain variables which show the parameters being passed to GGPLOT. I want to achieve following

  1. Printing the value of variables to browser underneath the plot or above plot
  2. Write a CSV file containing these variables and download it.

Hope I have explained my question correctly. I am copying sample code underneath

///////////////////////////////////////////////////////////////////////////////////////////////////////////

Global variables can go here

options(scipen=999)
library(survival)

# Define the UI

ui <- bootstrapPage(
titlePanel("Survival analysis step1"),
tags$hr(),
sidebarPanel(
fileInput("file1", "Choose CSV File",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),

 # Horizontal line ----
 tags$hr(),
 
 # Input: Checkbox if file has header ----
 checkboxInput("header", "Header", TRUE),
 
 # Input: Select separator ----
 radioButtons("sep", "Separator",
              choices = c(Comma = ",",
                          Semicolon = ";",
                          Tab = "\t"),
              selected = ","),
 
 # Input: Select quotes ----
 radioButtons("quote", "Quote",
              choices = c(None = "",
                          "Double Quote" = '"',
                          "Single Quote" = "'"),
              selected = '"'),
 
 # Horizontal line ----
 tags$hr(),
 
 # Input: Select number of rows to display ----
 radioButtons("disp", "Display",
              choices = c(Head = "head",
                          All = "all"),
              selected = "head")

),
mainPanel(
plotOutput('plot')
)
)

Define the server code

server <- function(input, output) {
output$plot <- renderPlot({

req(input$file1)

# when reading semicolon separated files,
# having a comma separator causes `read.csv` to error
    testdf <- read.csv(input$file1$datapath,
                   header = input$header,
                   sep = input$sep,
                   quote = input$quote)

#testdf<-read.csv("objective.csv",header = TRUE,na.strings=0)
testdf[is.na(testdf)]<-"0"
testdf$objl<-ifelse(as.numeric(testdf$obj_censor) ==2, as.numeric(testdf$objn), as.numeric(testdf$objl))
testdf$modified_objn<-ifelse(as.numeric(testdf$obj_censor) ==2, as.numeric(testdf$objl), as.numeric(testdf$objn))
set.seed(1234567)
testdf$Survial_analysis_obj<-Surv(as.numeric(testdf$modified_objn),as.numeric(testdf$objl), as.numeric(testdf$obj_censor), type="interval")
model_log_N_obj<-survreg(formula= testdf$Survial_analysis_obj~1, data=testdf, dist="lognormal")
new1<-data.frame(1)
predmodel_log_N_obj<-predict(model_log_N_obj, newdata=new1, type='quantile', p=seq(0.001,0.99, by=0.0001), se.fit=TRUE)

    plot(predmodel_log_N_obj$fit, seq(0.001,0.99, by=0.0001), 
     type="l", col=2, lty=1, lwd=2, xlim=c(0.00001,100000000), 
     main="Log-normal probability distribution models (objective symptoms)", 
     xlab="dose of peanut protein (mg)",
     ylab = "probability",  
     log="x", xaxt = "n", yaxt = "n") 
lines(exp(log(predmodel_log_N_obj$fit)+1.96* (predmodel_log_N_obj$se.fit)/ predmodel_log_N_obj$fit),seq(0.001,0.99, by=0.0001), type="l", col=2, lty=2)
lines(exp(log(predmodel_log_N_obj$fit)-1.96* (predmodel_log_N_obj$se.fit)/ predmodel_log_N_obj$fit),seq(0.001,0.99, by=0.0001), type="l", col=2, lty=2)

log_N_obj1<-predict(model_log_N_obj, newdata=new1, type='quantile', p=0.01, se.fit=TRUE) #0.18
#lower confidence level - 0.04
log_N_CL_obj1 <- exp(log(log_N_obj1$fit)-1.96* (log_N_obj1$se.fit)/ log_N_obj1$fit)
#upper confidence level - 0.75
log_N_CU_obj1<- exp(log(log_N_obj1$fit)+1.96* (log_N_obj1$se.fit)/ log_N_obj1$fit)

########### Trying to print and save these variables and write data frame into csv file
df<-data.frame(log_N_CU_obj1)
df$log_N_CL_obj1<-log_N_CL_obj1
df$log_N_obj1fit<-log_N_obj1$fit

})
visFun <- renderPrint(env=parent.frame(),{
log_N_obj1
}
)
visFun()
}

Return a Shiny app object

shinyApp(ui = ui, server = server)
///////////////////////////////////////////////////////////////////////////////////////////////////////////

2

You need something in the server to render the text into output list, then something in the ui to display this.

This page has an example
https://shiny.rstudio.com/tutorial/written-tutorial/lesson4/

By the way, to prevent your code looking terrible here, put three backticks ``` on a separate line before it and after it. This will create a proper code block.

3

Thanks Woodward, I will give it a try. in fact I was trying to do that I did not know how to render it on server and ui to display that because all calculations were done while I was trying to display the plot.

4

Hi Woodward,
I tried to do that, similar way and still my code contains the code the way I was doing but still no solution.

It gives an error that variable does not exist.
What I did in ui
textOutput("selected_var")

and then

output$selected_var <- renderText(ED01_log_N_obj)
or even tried following line as well

output$selected_var<-renderText({
ED01_log_N_obj
})

but still no issue. If you see in above main codes that the variables that does the printing of plot contains the variable. Do you think? I should try and move these variable outside renderPlot??

Thanks

5

That should work provided ED01_log_N_obj is a string. If it's not a string you need to turn it into string. It looks like it might be a model object? Maybe print(ED01_log_N_obj)?

The curly brackets {} allow you to have more than one statement or a whole block of code in place of the expression, and it will render the last thing in that block of code.

And format your code correctly, it looks like a mess on here. Put the backticks before and after like I told you. RStudio has an Addin on the tool bar, "Style active file", maybe you should use it.

6

Thanks @woodward, I will give it a try. Because I am posting first time so I did not know how to copy, paste code inside the editor. Thanks a lot for your suggestions.

7

The main editor features to know are single backticks around inline code like this and triple backticks aruond block code like

this
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8

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