Using renderUI in Shiny to display vectors - html

I want to be able to display a dynamic vector as text output in my Shiny app. I also want to utilize HTML (bold, font colors, etc.), so I am using htmlOutput and renderUI instead of textOutputand renderText per this suggestion.
Here is some example code:
library(shiny)
shinyApp(
ui <- htmlOutput("example"),
server <- function(input, output, session){
# vector (in the real app, this is not a static vector--it will be updated with other inputs)
states <- c("Alabama", "Alaska", "Arizona", "Arkansas")
# text output
output$example <- renderUI({
x <- paste0("<strong>Here are your states</strong>: ", states)
HTML(x)
}) #END RENDERUI
} #END SERVER
) #END SHINYAPP
The result of this code is:
Here are your states: Alabama Here are your states: Alaska Here are
your states: Arizona Here are your states: Arkansas
What I want is :
Here are your states: Alabama Alaska Arizona Arkansas
I have come up with a solution using conditional statements, but it's pretty clunky. Here's what I put in renderUI for the above desired output:
x <- paste0("<strong>Here are your states: </strong>",
if(!is.na(states[1])){states[1]},
if(!is.na(states[2])){states[2]},
if(!is.na(states[3])){states[3]},
if(!is.na(states[4])){states[4]})
HTML(x)
Again, the above solution works, but it's rather clunky and will be terribly inefficient for larger vectors (with, let's say, 10+ elements). Is there an easier way to display these vectors while still being able to utilize HTML?

You are looking for paste(..., collapse = " ").
library(shiny)
shinyApp(
ui <- htmlOutput("example"),
server <- function(input, output, session){
# vector (in the real app, this is not a static vector--it will be updated with other inputs)
states <- c("Alabama", "Alaska", "Arizona", "Arkansas")
# text output
output$example <- renderUI({
x <- paste0("<strong>Here are your states</strong>: ", paste(states, collapse = " "))
HTML(x)
}) #END RENDERUI
} #END SERVER
) #END SHINYAPP

Related

How to render a special character using HTML in Shiny R?

I am trying to display a greek letter delta as a symbol.
The unicode and encoding can be found here.
output$text <- renderText({
HTML("Displaying greek letter delta as a symbol: \u0394")
})
This results in exactly the same string when rendered instead of a symbol. Same happens when using "Δ" or "Δ". Maybe someone knows how to correctly format text with special symbols when using HTML() in R, or share any documentation relating this?
The desired output is: "Displaying greek letter delta as a symbol: Δ"
Here is a minimal example:
library(shiny)
ui <- fluidPage(
textOutput("text")
)
server <- function(input, output, session) {
output$text <- renderText({
HTML("Displaying greek letter delta as a symbol: \u0394")
})
}
shinyApp(ui, server)
Important: if you need to use HTML elements such as <br>, you will need to follow #Stéphane Laurent's comment and use renderUi() and uiOutput().
library(shiny)
ui <- fluidPage(
uiOutput("text")
)
server <- function(input, output, session) {
output$text <- renderUI({
HTML("<p> Displaying greek letter delta as a symbol:<br> \u0394
</p>")
})
}
shinyApp(ui, server)
Created on 2022-06-01 by the reprex package (v2.0.1)
With:
R version 4.2.0 (2022-04-22 ucrt)
shiny_1.7.1
Running under: Windows 10 x64 (build 19044)

column_spec crashing PDF in Rmd output to both PDF and html in shiny app

EDIT: Because I had set the format options in a global function, I have to set either latex_options or bootstrap_options in the kable_styling() call. I was using bootstrap_options which wasn't being read by the latex. My work-around is to make the tables twice, once in a chunk for html, and once in a chunk for latex. Not great, but it works if I click the Knit button and choose Knit to PDF. However, it throws the original error when I try to run it in the shiny app.
I have created a test version (MiniTest) of my project. What I need to do is have a shiny app run with a tab that will produce an html file for a user-chosen (reactive) Country, and provide an Excel download (I have that working so kept it out of this example), and a PDF download. I knit in an .Rmd which chooses the format and allows for parameterization. (The shiny part was set up by someone else, from whom I took over this project when they left before finishing it.)
I use kable and kableExtra to create and format tables, as I heard it words for both html and LaTeX output. The HTML is more as less as I want it. I can knit either html or PDF, and it runs, BUT when in the shiny app, only the html portion works. I think I have narrowed down the PDF issue(s) to column_spec crashing the download. If I comment out the column_spec lines in t01 and t02, the Download PDF runs. But I need that formatting. I'm sorry, but I've lost track of all the sites I have searched.
In global.R, I set:
countries <- c("ABC", "DEF", "GHI", "JKL")
In the .Rmd, I have YAML set up (with two-space indents for Country and output types):
params:
Country: ABC
output:
pdf_document: default
html_document: default
Relevant .Rmd chunks and inline code include:
knitr::opts_chunk$set(echo = FALSE)
options(knitr.table.format = function() {
if (knitr::is_latex_output()) "latex" else "html"
})
library(shiny)
library(htmlwidgets)
library(shinythemes)
library(shinydashboard)
library(shinyjs)
library(shinycssloaders)
library(markdown)
library(tidyr)
library(tidyverse)
library(janitor)
library(kableExtra)
options(scipen = 999)
mini <- mtcars %>%
tibble::rownames_to_column(var = "car") %>%
mutate(Country = c(rep("ABC", 8), rep("DEF", 8), rep("GHI", 8), rep("JKL", 8)))
## https://bookdown.org/yihui/rmarkdown-cookbook/font-color.html
colorize <- function(x, color) {
if (knitr::is_latex_output()) {
## hack setting color='blue' instead of a hexcode with # that breaks the LaTeX code
sprintf("\\textcolor{%s}{%s}", color = 'blue', x) ## works, but isn't right blue
} else if (knitr::is_html_output()) {
sprintf("<span style='color: %s;'>%s</span>", color, x)
} else x
}
## make two tables with `kable` and `kableExtra`
new_title <- paste0("Dynamically Changing Country Name in column", params$Country)
t01 <- mini %>%
filter(Country == params$Country) %>%
select(car, mpg:hp) %>%
rename({{new_title}} := car) %>%
kable(align = c("l", "c", "c", "c", "c")) %>%
kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "condensed")) %>%
column_spec(1, bold = TRUE) %>%
column_spec(2:3, width = "5em") %>%
row_spec(0, color = "#2A64AB") %>%
row_spec(6, bold = TRUE)
t02_title <- paste0(params$Country, " Table with Dollar Signs in Var Names")
t02 <- mini %>%
filter(Country == params$Country) %>%
select(car, drat, wt) %>%
mutate(car = case_when(car == "Mazda RX4" ~ "Mazda RX4 (US\\$)*", TRUE ~ as.character(car))) %>%
## want to blank out column names - removing them entirely would be best, but it fails
kable(align = c("l", "r", "c"), escape = TRUE, col.names = c("", "", "")) %>%
kable_styling(full_width = FALSE, position = "left", bootstrap_options = c("striped", "condensed")) %>%
column_spec(1, bold = TRUE) %>%
column_spec(2, width = "10em") %>%
footnote(general = "*Never smart to start with an asterisk, but here we are", general_title = "")
## make two charts with `ggplot2`
chart1 <- mini %>%
filter(Country == params$Country) %>%
select(car, mpg:hp) %>%
ggplot2::ggplot(mapping = aes(x = mpg)) +
geom_col(aes(y = `cyl`, fill = "cyl"), color = "black")
c1_title <- paste0("Some fab title here for ", params$Country)
chart2 <- mini %>%
filter(Country == params$Country) %>%
select(car, vs:carb) %>%
ggplot2::ggplot(mapping = aes(x = carb)) +
geom_col(aes(y = `gear`, fill = "gear"), color = "black")
c2_title <- paste0("Another chart, ", params$Country)
## make a "tiny" LaTeX environment that is only generated for LaTeX output, with chunk setting `include = knitr::is_latex_output()`.
knitr::asis_output('\n\n\\begin{tiny}')
## Table 1
t01
I expect a PDF to pop up, but instead a Save File box pops up asking to save "DownloadPDF" with no file extension. The ui.R is supposed to name it as "FactCountryName.pdf" where "CountryName" is input from the Country the user chose in the drop-down list. Regardless of whether I choose Save (nothing happens) or Cancel, my R throws the following error:
```
! LaTeX Error: Illegal character in array arg.
```
If I comment out the line column_spec(1, bold = TRUE) %>%, the error changes to:
```
! Use of \#array doesn't match its definition.
\new#ifnextchar ...served#d = #1\def \reserved#a {
#2}\def \reserved#b {#3}\f...
l.74 ...m}|>{\centering\arraybackslash}p{5em}|c|c}
```
Please help!
Turns out that using the Knit button in R automatically loads the required LaTeX packages, such as booktabs. Running the file in the Shiny app was not loading all the packages needed. All I had to do was specifically call the extra packages in the YAML (which I found by looking at the .tex file made from the PDF through Knit button).
---
params:
Country: ABC
header-includes:
- \usepackage{booktabs}
- \usepackage{longtable}
- \usepackage{array}
- \usepackage{multirow}
- \usepackage{wrapfig}
- \usepackage{float}
- \usepackage{colortbl}
- \usepackage{pdflscape}
- \usepackage{tabu}
- \usepackage{threeparttable}
- \usepackage{threeparttablex}
output:
pdf_document:
keep_tex: true
html_document: default
---

Integrating R outputs in bsplus functions

I consider bsplus package as relevant when developing dynamic webs. I use R Markdown in Rstudio.
However, I find particularly tricky the way to integrate bsplus functions with R outputs.
Let's see an example with the bs_accordion function, using mtcars dataset
head <- head(mtcars)
tail <- tail(mtcars)
bs_accordion(id ="Data: mtcars") %>%
bs_append(title = "Head of mtcars", content = head) %>%
bs_append(title = "Tail of mtcars", content = tail)
I would like to display R outputs in the accordion function, displaying the data frames head and tail.
Now, it only displays the first numerical row in the head.
Is there any possibility to include R code within the content attribute in the bsplus functions?
In this way we could be able to display R results in a dynamic way.
This should work for your example. You have to create a datatable somehow, just including it wont render it as a table.
Note: I changed the id of the accordion to Data-mtcars. Using a whitespace, ":" or ";" will disable the collapsing.
library(shiny)
library(bsplus)
library(DT)
ui <- fluidPage(
bs_accordion(id ="Data-mtcars") %>%
bs_set_opts(panel_type = "primary", use_heading_link = T) %>%
bs_append(title = "Head of mtcars", content = DT::dataTableOutput("table1")) %>%
bs_set_opts(panel_type = "primary", use_heading_link = T) %>%
bs_append(title = "Tail of mtcars", content = DT::dataTableOutput("table2"))
)
server <- function(input, output) {
output$table1 <- DT::renderDataTable({
head
})
output$table2 <- DT::renderDataTable({
tail
})
}
shinyApp(ui, server)

how dynamically read image file shiny R

I'm downloading a png image according to user provided input, and I show the image with
mainPanel(
img(src="file.png", height =1187 , width = 748)
)
but, if the user changes the input I have to refresh the page.
The app draft is follows below
the ui
library(shiny)
org <- read.delim("http://rest.kegg.jp/list/organism", header=FALSE)
org <- apply(org[,2:3], 1, function(x) paste(as.matrix(x), collapse="-"))
# Define UI for dataset viewer application
shinyUI(fluidPage(
# Application title
titlePanel("Reactivity"),
# Sidebar with controls to provide a caption, select a dataset, and
# specify the number of observations to view. Note that changes made
# to the caption in the textInput control are updated in the output
# area immediately as you type
sidebarLayout(
sidebarPanel(
textInput("caption", "Caption:", "Data Summary"),
tags$textarea(id="foo", rows=3, cols=40, "Default value"),
selectInput("dataset", "Choose an organism:",
choices = org ),
numericInput("obs", "Number of observations to view:", 10)
),
# Show the caption, a summary of the dataset and an HTML table with
# the requested number of observations
mainPanel(
h3(textOutput("caption")),
verbatimTextOutput("summary"),
tableOutput("view"),
plotOutput('plot1'),
img(src="file.png", height =1187 , width = 748)
)
)
))
and the server
library(shiny)
# Define server logic required to summarize and view the selected dataset
shinyServer(function(input, output) {
output$caption <- renderText({
cps <- strsplit(input$foo, "\\s+")[[1]]
#tab <- read.table("http://rest.kegg.jp/link/pathway/zma")
#path2cpd <- read.table("http://rest.kegg.jp/link/pathway/compound")
#allmetab <- unique(path2cpd[which(path2cpd[,2] %in% sub("path:zma", "path:map", tab[,2])),])
#cps <- unique(allmetab[,1])
#
url <- "http://www.kegg.jp/kegg-bin/show_pathway?zma00944+default%3dred+"
url <- paste(url, paste(cps, collapse="+"), sep="+")
download.file(url, "form.html")
lines <- readLines("form.html")
imgUrl <- lines[grep('img src="/', lines)]
url <- paste0("http://www.kegg.jp/", strsplit(imgUrl, '"')[[1]][2])
download.file(url, "www/file.png")
url
})
# The output$summary depends on the datasetInput reactive expression,
# so will be re-executed whenever datasetInput is invalidated
# (i.e. whenever the input$dataset changes)
output$plot1 <- renderPlot({
})
})
if you paste the compound codes
C01477
C04608
C04858
C05622
in the box with "Default Value" written I would like to automatically update the picture, or at least have a button to update without having to reload all the app.
If one reloads the navigator one can see the figure with the red dots colored (at the page bottom).
How can I make the function read the image again after a time interval?

Hide renderPrint Pre Tag Output from Shiny Application in R

I am developing a Shiny application in R. For certain pieces of renderPrint output I would like the shiny user interface to display nothing. Kind of like the hidden option for pre or div tags in HTML5 example shown below:
http://www.w3schools.com/tags/tryit.asp?filename=tryhtml5_global_hidden
Below is my shiny example code. A brief explanation: you can use a drop down menu to select one of two variables (factor variable or continuous variable). If you select the factor variable I want to show the caption and the table output. If you select the continuous variable I don't want to see anything. Right now, the caption disappears if you insert a blank string "" as the return to renderText. However, I don't know how to get renderPrint to show nothing. I've tried:
"". Doesn't work as it returns the actual blank string
NULL. Doesn't work as it returns the string NULL
invisible(). Best so far, but still doesn't work as it returns the grey formatted box.
Goal is to just display nothing. Shiny ui.r and server.r code given below:
library(shiny)
##
## Start shiny UI here
##
shinyUI(pageWithSidebar(
headerPanel("Shiny Example"),
sidebarPanel(
wellPanel(
selectInput( inputId = "variable1",label = "Select First Variable:",
choices = c("Binary Variable 1" = "binary1",
"Continuous Variable 1" = "cont1"),
selected = "Binary Variable 1"
)
)
),
mainPanel(
h5(textOutput("caption2")),
verbatimTextOutput("out2")
)
))
##
## Start shiny server file and simulated data here
##
binary1 <- rbinom(100,1,0.5)
cont1 <- rnorm(100)
dat <- as.data.frame(cbind(binary1, cont1))
dat$binary1 <- as.factor(dat$binary1)
dat$cont1 <- as.numeric(dat$cont1)
library(shiny)
shinyServer(function(input, output) {
inputVar1 <- reactive({
parse(text=sub(" ","",paste("dat$", input$variable1)))
})
output$caption2 <- renderText({
if ( (is.factor(eval(inputVar1()))==TRUE) ) {
caption2 <- "Univariate Table"
} else {
if ( (is.numeric(eval(inputVar1()))==TRUE) ) {
caption2 <- ""
}
}
})
output$out2 <- renderPrint({
if ( (is.factor(eval(inputVar1()))==TRUE) ) {
table(eval(inputVar1()))
} else {
if ( (is.numeric(eval(inputVar1()))==TRUE) ) {
invisible()
}
}
})
})
A few questions...
Why does renderText handle hidden/invisible presentation different than renderPrint? Is it because the former outputs text as pre tag; whereas, the latter displays formatted output in div tag?
To those HTML experts (upfront, I am not one)...what option would be best to get my output to display nothing? Is the hidden option embedded in a pre or div tag best (I know it doesn't work in IE browsers). Should I try something else? CSS options, etc?
Assuming hidden is the best way to go (or that I get an answer to 2. above), how do I pass this option/argument through the renderPrint function in shiny? Or would I need to use a different shiny function to achieve this functionality?
Btw...My R version is: version.string R version 3.0.1 (2013-05-16) and I am using shiny version {R package version 0.6.0}. Thanks in advance for your help.
I am not sure that I have understood your question, but try the following:
here is the Ui first:
library(shiny)
ui <- fluidPage(pageWithSidebar(
headerPanel("Shiny Example"),
sidebarPanel(
wellPanel(
selectInput(inputId = "variable1",label = "Select First Variable:",
choices = c("Binary Variable 1" = "binary1",
"Continuous Variable 1" = "cont1"),
selected = "Binary Variable 1"
)
)
),
mainPanel(
h5(textOutput("caption2")),
verbatimTextOutput("out2", placeholder=TRUE)
)
))
Start shiny Server file and simulated data here:
binary1 <- rbinom(100,1,0.5)
cont1 <- rnorm(100)
dat <- as.data.frame(cbind(binary1, cont1))
dat$binary1 <- as.factor(dat$binary1)
dat$cont1 <- as.numeric(dat$cont1)
server <- (function(input, output) {
inputVar1 <- reactive({
parse(text=sub(" ","",paste("dat$", input$variable1)))
})
output$caption2 <- renderText({
if ((is.factor(eval(inputVar1()))==TRUE) ) {
caption2 <- "Univariate Table"
} else {
if ((is.numeric(eval(inputVar1()))==TRUE) ) {
caption2 <- "Continous"
}
}
})
output$out2 <- renderPrint({
if ((is.factor(eval(inputVar1()))==TRUE) ) {table(eval(inputVar1()))}
})
})
And finally:
shinyApp(ui = ui, server = server)