caching plots in R/Shiny

问题

Just wondering if there are tricks/ways in which I could cache the plots being generated through our shiny app.

Background:

We are doing somewhat compute intensive computations which finally result in a plot. I am already caching(using memoise) the computations done, globally in shiny but it still takes about .75 seconds to render a plot. I was just wondering if we can decrease that time by removing the time it takes to render an image and if there are slick ways of already doing it.

More details:

I am using grid to create the plot(heatmap in this case. Ideally would like the caching to be disk based as storing plots in memory wont scale up.

Thanks! -Abhi

回答1:

Assuming you are using ggplot (which with Shiny, I would bet is a fair assumption).

Create an empty list to store your grob, say Plist.
When a user request a graph, create a string hash based on the shiny inputs
Check if the graph is already saved, eg hash %in% names(Plist)
If yes, serve up that graph
If no, generate the graph, save the grob to the list, name the element by the hash, eg, Plist[hash] <- new_graph

回答2:

Edit

Caching of images created with renderPlot()/plotOutput() is supported since shiny 1.2.0.

release notes: https://shiny.rstudio.com/reference/shiny/1.2.0/upgrade.html
function documentation https://shiny.rstudio.com/reference/shiny/1.2.0/renderCachedPlot.html.

The solution below behaves similar to the following usage of renderCachedPlot().

output$plot <- renderCachedPlot(
  expr = {
    histfaithful(bins = input$bins, col = input$col) 
  },
  cache = diskCache()
)

renderCachedPlot() allows caching in memory and on disk with sensible defaults. The rules for generating hash keys can be customized and by default digest::digest() is used for all reactive expressions that appear in expr.

The solution below demonstrates how a subset of these features (caching on disk) can be implemented with a shiny module. The basic strategy is to use

digest::digest() to create cache keys based on arguments sent to a plot function
do.call() to pass the arguments to the plot function unless the key created from digest() signifies that the image is already cached
grDevices::png() to capture an image from the call to do.call() and add it to the cache
shiny::renderImage() to serve images from the cache

Original answer

Although both answers to this question are very good, I wanted do add another one using shiny modules. The following module takes a plotfunction and a reactive version of it's arguments as inputs. In the end do.call(plotfun, args()) is used to create the plot.

library(shiny)

cachePlot <- function(input, output, session, plotfun, args, width = 480, height = 480,
                      dir = tempdir(), prefix = "cachedPlot", deleteonexit = TRUE){
  hash <- function(args) digest::digest(args)

  output$plot <- renderImage({
    args <- args()
    if (!is.list(args)) args <- list(args)
    imgpath <- file.path(dir, paste0(prefix, "-", hash(args), ".png"))

    if(!file.exists(imgpath)){
      png(imgpath, width = width, height = height)
      do.call(plotfun, args)
      dev.off()
    }
    list(src = imgpath)
  }, deleteFile = FALSE)

  if (deleteonexit) session$onSessionEnded(function(){
    imgfiles <- list.files(dir, pattern = prefix, full.names = TRUE)
    file.remove(imgfiles)
  })
}

cachePlotUI <- function(id){
  ns <- NS(id)
  imageOutput(ns("plot"))
}

As we can see, the module deletes the image files created if needed and gives the option to use a custom caching-directory in case persistent caching is needed (as it is in my actual usecase).

For a usage example, I'll use the hist(faithful[, 2]) example just like Stedy.

histfaithful <- function(bins, col){
  message("calling histfaithful with args ", bins, " and ", col) 
  x  <- faithful[, 2]
  bins <- seq(min(x), max(x), length.out = bins + 1)
  hist(x, breaks = bins, col = col, border = 'white')
}

shinyApp(
  ui = fluidPage(
    inputPanel(
      sliderInput("bins", "bins", 5, 30, 10, 1),
      selectInput("col", "color", c("blue", "red"))
    ),
    cachePlotUI("cachedPlot")
  ),
  server = function(input, output, session){
    callModule(
      cachePlot, "cachedPlot", histfaithful, 
      args = reactive(list(bins = input$bins, col = input$col))
    )
  }
)

回答3:

The answer from Ricardo Saporta is very good and what I used to solve a similar problem, but I wanted to add a code solution as well.

For caching I used digest::digest() where I just fed a list of the parameters for that particular graph to that function to create a hash string. I initially thought that I would have to extract the hash string from observe() and then use an if/else statment to determine if I should send it to renderImage() or renderPlot() based on if the image had previously been created. I flailed with this for a while and then stumbled upon just using renderImage(). Its not a perfect image substitution but more than close enough for the purposes of this demo.

ui.R

library(shiny)

fluidPage(
  sidebarLayout(
    sidebarPanel(
       sliderInput("bins",
                   "Number of bins:",
                   min = 1,
                   max = 50,
                   value = 25),
      selectInput("plot_color", "Barplot color",
                   c("green"="green",
                      "blue"="blue"))
    ),
    mainPanel(
       plotOutput("distPlot", width='100%', height='480px')
    )
  )
)

and server.R

library(shiny)

function(input, output) {

base <- reactive({
  fn <- digest::digest(c(input$bins, input$plot_color))
  fn})

output$distPlot <- renderImage({
    filename <- paste0(base(), ".png")
    if(filename %in% list.files()){
      list(src=filename)
    } else {
    x  <- faithful[, 2]
    bins <- seq(min(x), max(x), length.out = input$bins + 1)
    png(filename)
    hist(x, breaks = bins, col = input$plot_color, border = 'white')
    dev.off()
list(src=filename)
    }

  }, deleteFile = FALSE)
}

来源：https://stackoverflow.com/questions/24192570/caching-plots-in-r-shiny

标签

Shiny

shiny-server