OK; I made BiocParallel a little easier to use (bpiterate() can now
take as its first argument a vector; it does not need to have an
'iterator' function). One needs to install the 'devel' version of the
package, currently
BiocManager::install("Bioconductor/BiocParallel")
Here's the complete example
library(shiny)
library(BiocParallel)
server <- function(input, output) {
output$plot <- renderPlot({
input$goPlot # Re-run when button is clicked
withProgress(message = 'Making plot', value = 0, {
## Number of times we'll go through the loop
n <- 100
dat <- bpiterate(
seq_len(n),
function(i) {
Sys.sleep(.1)
data.frame(x = rnorm(1), y = rnorm(1))
},
REDUCE = function(x, y) {
incProgress(1/n)
rbind(x, y)
},
BPPARAM = SnowParam(tasks = n)
)
})
plot(dat$x, dat$y)
})
}
ui <- shinyUI(basicPage(
plotOutput('plot', width = "300px", height = "300px"),
actionButton('goPlot', 'Go plot')
))
shinyApp(ui = ui, server = server)
One thing about Henrik's suggestion is that it uses a number of
packages in addition to BiocParallel; if going that route maybe it
makes sense just to use those different packages rather than trying to
use them AND BiocParallel...
Martin
On Thu, Jul 7, 2022 at 8:32 AM Giulia Pais <giuliapa...@gmail.com> wrote:
>
> Thanks for the reply,
>
> By just playing a little with some test code it seems like the approach
> suggested by @Henrik Bengtsson is pretty straightforward so I’ll try with
> this one,
>
> Thanks again to everyone and have a nice day
>
>
>
> Giulia
>
>
>
> From: Martin Morgan <mtmorgan.b...@gmail.com>
> Date: Thursday, July 7, 2022 at 14:28
> To: Giulia Pais <giuliapa...@gmail.com>, Henrik Bengtsson
> <henrik.bengts...@gmail.com>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] BiocParallel and Shiny
>
> I think it should be straight-forward to use bpiterate() where the REDUCE
> function is evaluated locally. It might take a bit of care to make sure that
> the progress bar is actually informative – generally, increase the `tasks=`
> argument to the number of time you’d like the progress bar to be updated.
>
>
>
> iter <- function(n) {
>
> ## return the numbers n, n-1, n-2, … until n < 0, and then return NULL
>
> force(n)
>
> function() {
>
> if (n < 0)
>
> NULL
>
> else {
>
> n <<- n - 1
>
> n + 1
>
> }
>
> }
>
> }
>
>
>
> bpiterate(
>
> iter(10),
>
> function(i) { Sys.sleep(i/10); i },
>
> REDUCE = function(x, y) {
>
> message(y)
>
> c(x, y)
>
> },
>
> BPPARAM = SnowParam(workers = 2, tasks = 10)
>
> )
>
>
>
> Replace `message()` to do whatever is required to iterate the progress bar in
> shiny. There is a `reduce.in.order=` argument that might be necessary to
> obtain results in order; I’m not exactly sure how this would impact a
> progress bar when, for instance, the early tasks take a long time…
>
>
>
> Martin
>
>
>
>
>
> From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Giulia Pais
> <giuliapa...@gmail.com>
> Date: Thursday, July 7, 2022 at 6:11 AM
> To: Henrik Bengtsson <henrik.bengts...@gmail.com>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] BiocParallel and Shiny
>
> Thank you so much! I'll look into it, have a nice day
>
> Giulia Pais
> ________________________________
> From: Henrik Bengtsson <henrik.bengts...@gmail.com>
> Sent: Thursday, July 7, 2022 11:59:36 AM
> To: Giulia Pais <giuliapa...@gmail.com>
> Cc: Vincent Carey <st...@channing.harvard.edu>; bioc-devel@r-project.org
> <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] BiocParallel and Shiny
>
> Hi.
>
> If you use the DoparParam backend for BiocParallel with
> doFuture::registerDoFuture(), then you have access to everything
> available in the 'future' ecosystem. This means you can use any of
> the available future parallel backends, plus near-live progress
> updates via the 'progressr' package. Progress signaled by 'progressr'
> can be rendered in Shiny.
>
> See https://progressr.futureverse.org/#biocparallelbplapply---parallel-lapply,
> for an example how to use BiocParallel on top of the future framework
> together with progress updates signaled by 'progressr'.
>
> See https://progressr.futureverse.org/reference/withProgressShiny.html
> for progressr::withProgressShiny(), which is a plug-in replacement for
> shiny::withProgress(). Run example("withProgressShiny", package =
> "progressr") for an example.
>
> I gave a short presentation on progressr, with a focus on its use
> together with future, at eRum 2020. The talk is available at
> https://www.jottr.org/2020/07/04/progressr-erum2020-slides/. It might
> give some more insight on how it all works.
>
> Hope this helps,
>
> Henrik
>
> On Thu, Jul 7, 2022 at 11:51 AM Giulia Pais <giuliapa...@gmail.com> wrote:
> >
> > Hi, thanks for the reply.
> > Yes I�ve looked at this article, it seems to me like I have to access to
> > the �status� of a worker in order to do that, correct?
> > I mean, is there a way through BiocParallel interface in which I can
> > receive a notification when a worker has finished a task? It is not clear
> > to me how BiocParallel manages to update the progress bar internally � I
> > guess the mechanism is similar to the one I described: distribute workload
> > � when a worker has finished a task notify and update progress bar by one
> > tick.
> > I�m honestly not too practical with asynch task management in R, sorry.
> >
> > Thank you
> >
> > From: Vincent Carey <st...@channing.harvard.edu>
> > Date: Thursday, July 7, 2022 at 11:40
> > To: Giulia Pais <giuliapa...@gmail.com>
> > Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> > Subject: Re: [Bioc-devel] BiocParallel and Shiny
> > Interesting question. Have you looked at
> > https://shiny.rstudio.com/articles/progress.html ...? There is
> > also a file called progress.R in BiocParallel/R folder. Probably some new
> > code needs to be written
> > to connect information from the BiocParallel activities to the server so
> > incProgress is run as needed.
> >
> > On Thu, Jul 7, 2022 at 4:48 AM Giulia Pais
> > <giuliapa...@gmail.com<mailto:giuliapa...@gmail.com>> wrote:
> > Hello,
> > I have a question on the use of BiocParallel with Shiny: I would like to
> > show a progress bar on the UI much like the standard progress bar that can
> > be set in functions like bplapply() � is it possible to do it and how? I
> > haven�t found anything on the topic in the documentation unfortunately.
> >
> > Thanks in advance,
> > Giulia Pais
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> > The information in this e-mail is intended only for th...{{dropped:21}}
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