I want to output Shiny app as a PDF report. But R Markdown gives the following error "Warning: Error in eval: object 'plot2' not found".
The plot works in Shiny, I'm not too familiar with Markdown and I'm getting really frustrated since I feel like I have tried quite a few potential solutions. What am I doing wrong?
Shiny UI
library(ggplot2)
library(tidyr)
library(DBI)
library(RODBCext)
library(shiny)
library(knitr)
library(kableExtra)
ui <- fluidPage(
pageWithSidebar(
headerPanel(""),
sidebarPanel(
textInput("Table", ""),
downloadButton("downloadData", "Download"),
submitButton(text="Submit"),
mainPanel(
tabsetPanel(
tabPanel("Data", tableOutput("tTable"))
),
tabsetPanel(
tabPanel("Graph", plotOutput("plot1")
)
)
)
Shiney Server
server <- function(input, output, session)
{
SQLData <- reactive({
#SQL Query
})
output$tTable <- renderTable(SQLData())
output$plot1 <- renderPlot({
da <- gather(SQLData(), key=Result, 'Control', 'Sample'
)
da2 <- data.frame(da)
ggplot(da2,aes(x=Result,y=Control, color=Result))+geom_point(size = 5) + scale_y_continuous(limits = c(80, 120)) +labs(y="", x = "")})
output$downloadData <- downloadHandler(
filename = "report.pdf",
content = function(file)
{ params <- list(table = SQLData(),
plot2 = {
da <- gather(SQLData(), key=Result, 'Control', 'Sample'
)
da2 <- data.frame(da)
ggplot(da2,aes(x=Result,y=Control, color=Result))+geom_point(size = 5) + scale_y_continuous(limits = c(80, 120)) +labs(y="", x = "")})}
)
rmarkdown::render(input = "Report.Rmd",
output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
}
shinyApp(ui = ui, server = server)
R Markdown Report
---
title: "Report"
output: pdf_document
header-includes:
- \usepackage{float}
- \usepackage{booktabs}
- \usepackage{makecell}
params:
table: NA
plot2: NA
---
```{r echo = FALSE, eval = TRUE}
kable(params$table, format="latex", booktabs=TRUE) %>%
kable_styling(latex_options="scale_down")
```{r echo = FALSE, eval = TRUE}
library(ggplot2)
print(plot2)
Related
This question is quite basic and related to some questions before How to save reactive plot as png to working directory in a shiny app
I had to change my strategy creating a plot from a shiny app in Rmarkdown.
For this I need to accomplish this simple task:
How can I save this plot to the temp folder as png?
Background: After saving to temp folder I will transfer it to R markdown to create a report.
library(shiny)
ui <- basicPage(
plotOutput("plot1"),
)
server <- function(input, output) {
output$plot1 <- renderPlot({
plot(mtcars$wt, mtcars$mpg)
})
}
shinyApp(ui, server)
Update: My original code looks like this. I can't provide a reproducible example with this because it is to complex:
How can I implement the answer by ismirsehregal to this code:
# plot: Radarplot ------
output$radar <- renderChartJSRadar({
chartJSRadar(PSA_13()[,c(1,2,6)],
main = "XXX",
maxScale = 100, scaleStepWidth = 10, scaleStartValue = 0, labelSize = 12,
addDots = TRUE, showToolTipLabel = TRUE, showLegend = TRUE, lineAlpha = 0.8,
polyAlpha = 0.2, responsive = FALSE,
colMatrix = col2rgb(c("orange", "navy" ,"grey")))
})
# create markdown report with radar plot ----------------------------------
output$report <- downloadHandler(
filename = "report.pdf",
content = function(file) {
td <- tempdir()
tempReport <- file.path(td, "report.Rmd")
tempLogo <- file.path(td, "logo.png")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
file.copy("logo.png", tempLogo, overwrite = TRUE)
params <- list(scores = PSA_13()[,c(1,2,6)])
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
report.Rmd
---
geometry: margin=20truemm
fontfamily: mathpazo
fontsize: 11pt
documentclass: article
classoption: a4paper
urlcolor: blue
output:
pdf_document
header-includes:
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \rhead{\includegraphics[width = .05\textwidth]{logo.png}}
params:
scores: NA
plot_object: NA
---
\pagenumbering{gobble}
```{r setup, include=FALSE}
knitr::opts_chunk$set()
library(draw)
```
```{r rectangle, echo=FALSE}
drawBox(x =1.3, y = 3.7, width = 2.5, height = 1)
```
\vspace{-80truemm}
```{r plotout, echo=FALSE, message=FALSE, out.width='100%'}
params$plot_object
```
<!-- ```{r, echo=FALSE, out.width="100%", } -->
<!-- chartJSRadar(params$scores, width = 700, height = 700, -->
<!-- main = "Peritoneal Surface Calculator Radarchart", -->
<!-- maxScale = 100, -->
<!-- scaleStepWidth = 10, -->
<!-- scaleStartValue = 0, -->
<!-- labelSize = 14, -->
<!-- addDots = TRUE, -->
<!-- showToolTipLabel = FALSE, -->
<!-- showLegend = TRUE, -->
<!-- lineAlpha = 0.8, -->
<!-- polyAlpha = 0.2, -->
<!-- responsive = FALSE, -->
<!-- colMatrix = col2rgb(c("orange", "navy" ,"grey"))) -->
<!-- ``` -->
I feel quite near to the solution and I am very grateful for your time!
There is no need to save a temporary png file. We can use recordPlot instead:
library(shiny)
library(datasets)
writeLines(con = "report.Rmd", text = "---
title: 'Plot report'
output: html_document
params:
plot_object: NA
---
```{r plotout, echo=FALSE, message=FALSE, out.width='100%'}
params$plot_object
```")
ui = fluidPage(
plotOutput("plot1"),
downloadButton("report_button", "Generate report")
)
server = function(input, output, session) {
reactivePlot1 <- reactive({
plot(mtcars$wt, mtcars$mpg)
recordPlot()
})
output$plot1 <- renderPlot({
reactivePlot1()
})
output$report_button <- downloadHandler(
filename = "report.html",
content = function(file) {
tempReport <- tempfile(fileext = ".Rmd") # make sure to avoid conflicts with other shiny sessions if more params are used
file.copy("report.Rmd", tempReport, overwrite = TRUE)
rmarkdown::render(tempReport, output_format = "html_document", output_file = file, output_options = list(self_contained = TRUE),
params = list(plot_object = reactivePlot1())
)
}
)
}
shinyApp(ui, server)
Please see my related answer here.
After OPs update - using dummy data:
app.R:
library(shiny)
library(radarchart)
scores <- data.frame("Label"=c("Communicator", "Data Wangler", "Programmer",
"Technologist", "Modeller", "Visualizer"),
"Rich" = c(9, 7, 4, 5, 3, 7),
"Andy" = c(7, 6, 6, 2, 6, 9),
"Aimee" = c(6, 5, 8, 4, 7, 6))
ui = fluidPage(
chartJSRadarOutput("radar", width = "450", height = "300"),
downloadButton("report", "Generate report")
)
server = function(input, output, session) {
reactiveRadar <- reactive({
chartJSRadar(scores, maxScale = 10, showToolTipLabel=TRUE)
})
# plot: Radarplot ------
output$radar <- renderChartJSRadar({
reactiveRadar()
})
# create markdown report with radar plot ----------------------------------
output$report <- downloadHandler(
filename = "report.html",
content = function(file) {
td <- tempdir()
tempReport <- file.path(td, "report.Rmd")
# tempLogo <- file.path(td, "logo.png")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
# file.copy("logo.png", tempLogo, overwrite = TRUE)
params <- list(scores = "Test", plot_object = reactiveRadar()) # scores = PSA_13()[,c(1,2,6)]
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
}
shinyApp(ui, server)
report.Rmd:
---
geometry: margin=20truemm
fontfamily: mathpazo
fontsize: 11pt
documentclass: article
classoption: a4paper
urlcolor: blue
output:
html_document
header-includes:
- \usepackage{fancyhdr}
- \pagestyle{fancy}
# - \rhead{\includegraphics[width = .05\textwidth]{logo.png}}
params:
scores: NA
plot_object: NA
---
\pagenumbering{gobble}
```{r setup, include=FALSE}
knitr::opts_chunk$set()
library(draw)
```
```{r rectangle, echo=FALSE}
drawBox(x =1.3, y = 3.7, width = 2.5, height = 1)
```
\vspace{-80truemm}
```{r plotout, echo=FALSE, message=FALSE, out.width='100%'}
params$plot_object
```
There are multiple options here.
In your case you could go with a simple option like this:
library(shiny)
ui <- basicPage(
plotOutput("plot1"),
actionButton("save", "Click to save")
)
server <- function(input, output) {
output$plot1 <- renderPlot({
plot(mtcars$wt, mtcars$mpg)
})
observeEvent("save", {
png('C:/path/to/your_plot/plot_saved.png')
plot(mtcars$wt, mtcars$mpg)
dev.off()
})
}
shinyApp(ui, server)
If you want to specify size, resolution, etc. you will have to customize the code within the observeEvent
I am trying to adapt the RMarkdown file with *.rmd extension into Shiny application. My file has elements of Shiny but works with flexdashboard. Below you can see the code.
---
title: "Test"
author: " "
output:
flexdashboard::flex_dashboard:
orientation: columns
social: menu
source_code: embed
runtime: shiny
editor_options:
markdown:
wrap: 72
---
# Module 1
```{r global, include=FALSE}
library(biclust)
data(BicatYeast)
set.seed(1)
res <- biclust(BicatYeast, method=BCPlaid(), verbose=FALSE)
```
## Inputs {.sidebar}
```{r}
selectInput("clusterNum", label = h3("Cluster number"),
choices = list("1" = 1, "2" = 2),
selected = 1)
```
## Row {.tabset}
### Parallel Coordinates
```{r}
num <- reactive(as.integer(input$clusterNum))
renderPlot(
parallelCoordinates(BicatYeast, res, number=num()))
```
### Data for Selected Cluster
```{r}
renderTable(
BicatYeast[which(res#RowxNumber[, num()]), which(res#NumberxCol[num(), ])]
)
```
The shiny app usually has two main parts first is ui and second is server, so can anybody help how to solve this problem and run this file as a Shiny app.
library(shiny)
library(biclust)
ui <- fluidPage(
selectInput("clusterNum",
label = h3("Cluster number"),
choices = list("1" = 1, "2" = 2),
selected = 1
),
plotOutput("plot"),
tableOutput("table")
)
server <- function(input, output, session) {
set.seed(1)
data(BicatYeast)
res <- biclust(BicatYeast, method = BCPlaid(), verbose = FALSE)
num <- reactive(as.integer(input$clusterNum))
output$plot <-
renderPlot(
parallelCoordinates(BicatYeast, res, number = num())
)
output$table <-
renderTable(
BicatYeast[which(res#RowxNumber[, num()]), which(res#NumberxCol[num(), ])]
)
}
shinyApp(ui, server)
I am fairly new to R markdown. I have built an app that requires the user to provide multiple inputs to generate a table, which can then be saved locally.
I have been now asked to implement a sort of report to list all the variables inserted by the user (in a sort of formatted document), so that before generating the table one can review all the settings and change them in case of errors.
To avoid major UI restructure, I thought about using a r markdown document and visualize it inside a modal. My problem is that rmarkdown::render renders to an output, while bs_modal takes for the argument body a character (HTML) variable.
Is there a way to make this work? Or are there better way to accomplish this?
A minimal example:
my .Rmd
---
title: "Dynamic report"
output:
html_document: default
pdf_document: default
params:
n : NA
---
A plot of `r params$n` random points.
```{r, echo=FALSE}
plot(rnorm(params$n), rnorm(params$n))
```
My App.R
library(shiny)
library(bsplus)
library(rmarkdown)
shinyApp(
ui = fluidPage(
selectInput(
inputId = "numb",
label = "Label with modal help",
choices = 50:100
),
actionButton(inputId = "mysheet",
label = "Open modal") %>% bs_attach_modal(id_modal = "modal1"),
textOutput("result")
),
server = function(input, output) {
observeEvent(input$mysheet, {
params <- input$numb
md_out <-
rmarkdown::render(
"report.Rmd",
params = params,
envir = new.env(parent = globalenv())
)
bs_modal(
id = "modal1",
title = "Equations",
body = md_out,
size = "medium"
)
})
output$result <- renderText({
paste("You chose:", input$numb)
})
}
)
bs_modal does not work like this, it must be in the UI. Below is a solution using the classical Shiny modal, no bsplus or other package.
library(shiny)
shinyApp(
ui = fluidPage(
selectInput(
inputId = "numb",
label = "Label with modal help",
choices = 50:100
),
actionButton(inputId = "mysheet",
label = "Open modal"),
textOutput("result")
),
server = function(input, output) {
observeEvent(input$mysheet, {
params <- list(n = input$numb)
md_out <-
rmarkdown::render(
"report.Rmd",
params = params,
envir = new.env(parent = globalenv())
)
showModal(modalDialog(
includeHTML(md_out),
title = "Equations",
size = "m"
))
})
output$result <- renderText({
paste("You chose:", input$numb)
})
}
)
Use html_fragment as the Rmd output:
---
title: "Dynamic report"
output:
html_fragment
params:
n : NA
---
A plot of `r params$n` random points.
```{r, echo=FALSE}
plot(rnorm(params$n), rnorm(params$n))
```
I'm trying to make a reactive data table in R Shiny that has a button you can press to compile an RMarkdown document. Ultimately, I'm trying to combine the solutions from these two links:
R Shiny: Handle Action Buttons in Data Table and https://shiny.rstudio.com/articles/generating-reports.html. Here is what I have so far:
library(shiny)
library(shinyjs)
library(DT)
shinyApp(
ui <- fluidPage(
DT::dataTableOutput("data")
),
server <- function(input, output) {
useShinyjs()
shinyInput <- function(FUN, len, id, ...) {
inputs <- character(len)
for (i in seq_len(len)) {
inputs[i] <- as.character(FUN(paste0(id, i), ...))
}
inputs
}
df <- reactiveValues(data = data.frame(
Portfolio = c('Column1', 'Column2'),
Option_1 = shinyInput(downloadButton, 2, 'compile_', label = "Compile Document", onclick = 'Shiny.onInputChange(\"compile_document\", this.id)' ),
stringsAsFactors = FALSE,
row.names = 1:2
))
output$data <- DT::renderDataTable(
df$data, server = FALSE, escape = FALSE, selection = 'none', filter='top'
)
output$compile_document <- downloadHandler(
filename = "report.html",
content = function(file) {
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
params <- list(n = input$slider)
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
}
)
Here is the RMarkdown document I'd like to compile:
---
title: "Dynamic report"
output: html_document
params:
n: NA
---
```{r}
# The `params` object is available in the document.
params$n
```
A plot of `params$n` random points.
```{r}
plot(rnorm(params$n), rnorm(params$n))
```
The pieces all seem to be there, but I can't connect the "Compile Document" button to the download handler.
Here is a way that does not use downloadHandler.
library(shiny)
library(DT)
library(base64enc)
library(rmarkdown)
js <- '
Shiny.addCustomMessageHandler("download", function(b64){
const a = document.createElement("a");
document.body.append(a);
a.download = "report.docx";
a.href = b64;
a.click();
a.remove();
})
'
buttonHTML <- function(i){
as.character(
actionButton(
paste0("button_", i), label = "Report",
onclick = sprintf("Shiny.setInputValue('button', %d);", i)
)
)
}
dat <- data.frame(
PortFolio = c("Column 1", "Column 2")
)
dat$Action <- sapply(1:nrow(dat), buttonHTML)
ui <- fluidPage(
tags$head(tags$script(HTML(js))),
br(),
sliderInput("slider", "Sample size", min = 10, max = 50, value = 20),
br(),
DTOutput("dtable")
)
server <- function(input, output, session){
output[["dtable"]] <- renderDT({
datatable(dat, escape = -ncol(dat)-1)
})
observeEvent(input[["button"]], {
showNotification("Creating report...", type = "message")
tmpReport <- tempfile(fileext = ".Rmd")
file.copy("report.Rmd", tmpReport)
outfile <- file.path(tempdir(), "report.html")
render(tmpReport, output_file = outfile,
params = list(
data = dat[input[["button"]], -ncol(dat)],
n = input[["slider"]]
)
)
b64 <- dataURI(
file = outfile,
mime = "text/html"
)
session$sendCustomMessage("download", b64)
})
}
shinyApp(ui, server)
The rmd file:
---
title: "Dynamic report"
output: html_document
params:
data: "x"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Row contents:
```{r}
params$data
```
A plot of `params$n` random points:
```{r}
plot(rnorm(params$n), rnorm(params$n))
```
I am still learning R and thus would request the experts in this platform to help me out.
I am trying to create a slideshow of .jpg images in a panel in Shiny. The below code when I run in RStudio gives me the slideshow in the Plot window of RStudio.
folder <- "D:/Photos/Foreign Trips/2014_07_08_USA_Irvine/JulyAugust/"
file_list <- list.files(path=folder, pattern="*.jpg", full.names = TRUE)
for (j in 1:30) {
myJPG <- stack(file_list[[j]])
plotRGB(myJPG)
}
But, when I try to put the same code in server.R and try to call through ui.R, I don't get the slideshow or any image getting displayed. I am getting a blank page when I click on the tab "Photo Slides". I tried using renderUI, renderImage and renderPlot but none works.
ui.R
tabPanel("Photo Slides",
plotOutput("trvImg")
),
server.R
output$trvImg <- renderPlot({
folder <- "D:/Photos/Foreign Trips/2014_07_08_USA_Irvine/JulyAugust/"
file_list <- list.files(path=folder, pattern="*.jpg", full.names = TRUE)
for (j in 1:30) {
myJPG <- stack(file_list[[j]])
plotRGB(myJPG)
}
As a learner, I am sure I'm going wrong somewhere and thus seek your help.
Thanks
Another solution, with the slickR package (based on the slick javascript library).
library(shiny)
library(slickR)
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
####
),
mainPanel(
slickROutput("slickr", width="500px")
)
)
)
server <- function(input, output) {
output$slickr <- renderSlickR({
imgs <- list.files("D:/Photos/Foreign Trips/2014_07_08_USA_Irvine/JulyAugust/", pattern=".png", full.names = TRUE)
slickR(imgs)
})
}
# Run the application
shinyApp(ui = ui, server = server)
library(shiny)
imgs <- list.files("D:/Photos/Foreign Trips/2014_07_08_USA_Irvine/JulyAugust/", pattern=".png", full.names = TRUE)
ui <- fluidPage(
titlePanel("Slideshow"),
sidebarLayout(
sidebarPanel(
actionButton("previous", "Previous"),
actionButton("next", "Next")
),
mainPanel(
imageOutput("image")
)
)
)
server <- function(input, output, session) {
index <- reactiveVal(1)
observeEvent(input[["previous"]], {
index(max(index()-1, 1))
})
observeEvent(input[["next"]], {
index(min(index()+1, length(imgs)))
})
output$image <- renderImage({
x <- imgs[index()]
list(src = x, alt = "alternate text")
}, deleteFile = FALSE)
}
# Run the application
shinyApp(ui = ui, server = server)
If you want the buttons below the image, you can do:
sidebarLayout(
sidebarPanel(
# actionButton("previous", "Previous"),
# actionButton("next", "Next")
),
mainPanel(
imageOutput("image"),
fluidRow(
column(1, offset=1, actionButton("previous", "Previous")),
column(1, offset=1, actionButton("next", "Next"))
)
)
)
I wanted to do the same, but needed a static html output so couldn't use Shiny. I created a simple revealjs presentation and then included this in the flexdashboard as an iframe.
revealjs:
---
title:
output:
revealjs::revealjs_presentation:
transition: convex
reveal_options:
loop: true
autoSlide: 3000
keyboard: false
progress: false
shuffle: true
embedded: true
---
```{r setup, include=FALSE}
library(tidyverse)
library(glue)
library(pander)
```
```{r echo = FALSE, results ='asis'}
files <- list.files(path="./path/to/dir", full.names = TRUE)
headers <- lapply(files,
function(f){glue("{data-background='{{f}}'}",
.open = "{{",
.close = "}}")
})
pandoc.header(headers, 2)
```
Then in my flexdashboard I added:
```{r}
tags$iframe(style = "height:400px; width:100%; scrolling=yes",
src ="./imageSlider.html")
```