Unable to see images in rmarkdown table - r

Question

I am trying to create a downloadable report from a shiny app. The report shows a table in which there are images.
I am passing the table with the url in the table as a parameter to the report as follows:
server <- function(input, output,session) {
data <- reactive({
data <- data.frame(RV3$data[,input$Map_EndoscopistIn],
RV3$data[,input$Map_FindingsIn],
RV3$data[,input$Map_MicroscopicTextIn],
RV3$data$url)
names(data)<-c(input$Map_EndoscopistIn,input$Map_FindingsIn,input$Map_MicroscopicTextIn,"Image")
if(!is.null(input$EndoscopistChooserIn)){
data<-data%>%filter(get(input$Map_EndoscopistIn)==input$EndoscopistChooserIn)
}
data
})
}
output$report <- downloadHandler(
# For PDF output, change this to "report.pdf"
filename = "report.doc",
content = function(file) {
# Copy the report file to a temporary directory before processing it, in
# case we don't have write permissions to the current working dir (which
# can happen when deployed).
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
browser()
# Set up parameters to pass to Rmd document
params <- list(performanceTable=data()
)
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
the url column in data() contains the following path eg:
![](<img src='Images/Images Captured with Proc Data Audit.files/img2527.jpg'>)
The report is as follows:
---
title: "Dynamic report"
always_allow_html: yes
output:
word_document:
fig_caption: true
params:
performanceTable: NA
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
```
```{r,echo=FALSE,warning=FALSE}
pander(params$performanceTable, justify='left',split.table=Inf,caption="Table 1: Cancer diagnoses")
```
The report is in the same folder as the Images folder.
With this I get the following error example:
[pandoc warning] Could not find image `img%20src='Images/Images%20Captured%20with%20Proc%20Data%20Audit.files/img2500.jpg'', skipping...
What am I doing wrong? Is this a reformatting in pander issue or a paths issue or what? Or could this be that the report root is the tmp directory whereas I am referring to images stored in anoter static directory. If it is the latter, what do I do to get paths relative to the temp directory so I can see the images?

Answer 1

The reason you couldn't locate your image file is because you render your report.Rmd from a temp directory where your image doesn't exist:
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
The solution is that the image should also be copied to the same temp directory where markdown syntax ![](img.png) will pick up the file.
As in code change, you should be able to get it working by doing this:
assign a tempDir
tempDir <- tempdir()
Move Rmd as well as images to tempDir
file.copy(c("report.Rmd", "Images/Images Captured with Proc Data
Audit.files/img2527.jpg"), tempDir, overwrite = TRUE)
then render from temp dir
rmarkdown::render(file.path(tempDir, 'report.Rmd'), output_file = file,
params = params,
envir = new.env(parent = globalenv())