Passing user input in Shiny to a URL query string - r

Question

I have a question that I'm having trouble getting to work. I have a Shiny app that I want to accept two user input, send it back from ui.R to server.R, and insert that as a variable into a URL query string to download the file from a database. At first, we hardcoded the values to test the algorithm but we eventually want to make it user defined. I thought that saving as a variable and replacing it in the query string would work, but it didn't... I tried to concatenate pieces of the URL and I'm getting an error "Warning: Error in cat: argument 1 (type 'closure') cannot be handled by 'cat'". I tried to search online but couldn't find a good solution to my problem. Here is my code so far... As you see in the code, what I want to get is at least form the url and showing it as text on the ui just to see that it is being dynamic. Then when I know I can insert the user input, then I can continue on with storing the downloaded file.
#ui.R
library(shiny)
library(leaflet)
library(foreach)
library(ape)
library(data.table)
library(DT)
# Choices for the genetic distance model
geneticDistanceModel <- c(
"raw" = "raw",
"JC69" = "JC69",
"K80" = "K80",
"F81" = "F81",
"K81" = "K81",
"F84" = "F84",
"BH87" = "BH87",
"T92" = "T92",
"TN93" = "TN93",
"GG95" = "GG95",
"logdet" = "logdet",
"paralin" = "paralin"
)
shinyUI(navbarPage("TeMPuЯa", id="nav", position = c("fixed-top"),
# needed to keep fixed-top navbar from obscuring content
header = tags$style(type = "text/css", "body {padding-top: 70px;}"),
collapsible = "true",
tabPanel("Tool",
h1("Instructions"),
p("Placeholder"),
sidebarLayout(
sidebarPanel(
textInput("taxonomy", label = h4("Enter taxonomy group:"), value = "Porifera"),
textInput("geography", label = h4("Enter geographical location:"), value = "all"),
sliderInput("latitude", label = h4("Latitude difference"), min = 10, max = 30, value = 20),
sliderInput("genetic", label = h4("Genetic similarity threshold"), min = 10, max = 20, value = 15),
sliderInput("outgroups", label = h4("Select a distance from the outgroup"), min = 1, max = 2, value = 1.3, step = 0.1),
selectInput("distanceModels", label = h4("Select a genetic distance model"), geneticDistanceModel, selected = "K80"),
submitButton("Submit"),
br(),
downloadButton("download", label = "Download CSV")
),
mainPanel(
leafletOutput("worldmap"),
br(),
div(style='height:300px; width:850px; overflow:scroll',
DT::dataTableOutput("url", width = 850)),
textOutput("text")
)
)
),
tabPanel("Genetic Distance Models Info",
h1("Genetic distance models:"),
a("Link to more explanation for the distance models used in R", href = "http://svitsrv25.epfl.ch/R-doc/library/ape/html/dist.dna.html"),
br(),
p(strong("raw:") ,"This is simply the proportion or the number of sites that differ between each pair of sequences. This may be useful to draw 'saturation plots'."),
p(strong("JC69:") ,"This model was developed by Jukes and Cantor (1969)."),
p(strong("K80:") ,"The distance derived by Kimura (1980), sometimes referred to as 'Kimura's 2-parameters distance'."),
p(strong("F81:") ,"Felsenstein (1981) generalized the Jukes-Cantor model."),
p(strong("K81:") ,"This model is called the Kimura's 'three substitution types model' (3ST), and is sometimes referred to as 'Kimura's 3-parameters distance'."),
p(strong("F84:") ,"This model generalized K80, and was first introduced by Felsenstein in 1984."),
p(strong("BH87:") ,"Barry and Hartigan (1987)."),
p(strong("T92:") ,"Tamura (1992) generalized the Kimura model."),
p(strong("TN93:") ,"Tamura and Nei (1993) model."),
p(strong("GG95:") ,"Galtier and Gouy (1995) model."),
p(strong("logdet:") ,"The Log-Det distance, developed by Lockhart et al. (1994), is related to BH87. However, this distance is symmetric."),
p(strong("paralin:") ,"Lake (1994) developed the paralinear distance which can be viewed as another variant of the Barry-Hartigan distance.")
)
))
# server.R
library(shiny)
library(leaflet)
library(foreach)
library(ape)
library(data.table)
library(DT)
source("tsvtoDataFrame.R")
shinyServer(function(input, output, session) {
# Create the map
output$worldmap <- renderLeaflet({
leaflet() %>%
addTiles() %>% # Add default OpenStreetMap map tiles
setView(lng = -93.85, lat = 37.45, zoom = 4)
})
textInput <- reactive({
var1 <- "http://www.boldsystems.org/index.php/API_Public/combined?taxon="
var2 <- "&geo="
var3 <- "&format=tsv"
paste(c(var1), c(input$taxonomy), c(var2), c(input$geography), c(var3))
})
output$text <- renderText({
textInput
})
output$url <- DT::renderDataTable(
dfMatchOverallBest,
options = list(scrollX = TRUE)
)
})

Answer 1

textInput is a reactive, so you should use
output$text <- renderText({
textInput()
})
Also you should probably use paste0 instead of paste to get your URL, and the c() command is not necessary.