papayaWIdget for Shiny

[robertoromor]

Hi John,

I am having trouble rendering the papayaWidget on Shiny, it just shows a blank page, you will find my session on this link and below the code I am using:

robertoromo-sessioninfo.txt

code:

`library(kirby21.t1) library(papayaWidget) library(neurobase)

outdir = tempdir() download_t1_data(outdir = outdir)

fname = kirby21.t1::get_t1_filenames(outdir = outdir) fname = fname[3]

ui <- shinyUI( fluidPage( papayaOutput("test") ) )

server <- function(input, output, session) {

output$test<-renderPapaya({

img = readnii(fname)

print(img) papaya(img) })

}

shinyApp(ui, server)`

[muschellij2]

@adigherman ?

[adigherman]

I was able to replicate the problem on my end. Tracked this down to htmlwidgets.js (line 500) but I was not able to figure out how to fix it yet. Debugging htmlwidgets is not an easy task.

[robertoromor]

Hi guys, do yo have some example that works in shiny or some way around it?

[robertoromor]

@muschellij2 @adigherman Is there a way we can modify the papaya function to make it open up the widget in a browser directly??? or maybe there already is a parameter that does this.

[muschellij2]

What do you mean? As compared to the Viewer in RStudio? John

On Fri, Jul 12, 2019 at 3:01 PM robertoromor notifications@github.com wrote:

@muschellij2 https://github.com/muschellij2 @adigherman https://github.com/adigherman Is there a way we can modify the papaya function to make it open up the widget in a browser directly??? or maybe there already is a parameter that does this.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/muschellij2/papayaWidget/issues/6?email_source=notifications&email_token=AAIGPLWW4QBI5EBSSRM6KBDP7DIKLA5CNFSM4HPSDUEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZ2TM2A#issuecomment-510998120, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLQWCELCV3KPC2JILI3P7DIKLANCNFSM4HPSDUEA .

[robertoromor]

For example a new feature like this.

papaya(directory/image.dcm, viewe=c("browser", "Rstudio viewer"), ... )

The point is that if it is not possible to use the papayaviewer within a Shiny enviroment, I want to know if it is possible to call the papaya function (see above) within shiny for it to open in another tab within the browser where I am using shiny.

Roberto R.

[robertoromor]

I believe the feature is not there, I just want to know if it is possibile to tweak the function to have the feature I am mentioning, if so how difficult is this "tweak"

[muschellij2]

You'd have to open an issue with htmlwidgets I think. John

On Tue, Jul 16, 2019 at 5:13 PM robertoromor notifications@github.com wrote:

I believe the feature is not there, I just want to know if it is possibile to tweak the function to have the feature I am mentioning, if so how difficult is this "tweak"

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/muschellij2/papayaWidget/issues/6?email_source=notifications&email_token=AAIGPLXAUMO2DJNXD26SPD3P7Y2XRA5CNFSM4HPSDUEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2CFPXY#issuecomment-511989727, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLUOH3BLP2RRH7KOHULP7Y2XRANCNFSM4HPSDUEA .

[muschellij2]

Try this out with a new install of papayaWidget:

require(shiny)
require(WhiteStripe)
require(papayaWidget)

fnames = ws_img_data()
names(fnames) = neurobase::nii.stub(fnames, bn = TRUE)

server <- function(input, output) {
  output$plot <- renderPapaya({
    x = papaya(fnames)
    x$elementId = NULL
    x
  })
}

ui <- fluidPage(
  papayaOutput("plot")
)

shinyApp(ui = ui, server = server)

[robertoromor]

I tried it with the same result. A blank shinyapp

[muschellij2]

Works on my end - please send sessionInfo with all updates and also any example code. John

On Wed, Jul 24, 2019 at 4:17 PM robertoromor notifications@github.com wrote:

I tried it with the same result. A blank shinyapp

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/muschellij2/papayaWidget/issues/6?email_source=notifications&email_token=AAIGPLSN26SICADKTW7VULDQBC2GHA5CNFSM4HPSDUEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2XPUYA#issuecomment-514783840, or mute the thread https://github.com/notifications/unsubscribe-auth/AAIGPLTWJAREW3WSFNHW2HDQBC2GHANCNFSM4HPSDUEA .

[robertoromor]

session info below. Whay do you mean by "any example code"

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Mexico.1252  LC_CTYPE=Spanish_Mexico.1252    LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C                   
[5] LC_TIME=Spanish_Mexico.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] papayaWidget_0.5.4 WhiteStripe_2.3.1  shiny_1.2.0        RSQLite_2.1.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0         compiler_3.5.2     later_0.8.0        R.methodsS3_1.7.1  bitops_1.0-6       base64enc_0.1-3    R.utils_2.8.0     
 [8] tools_3.5.2        digest_0.6.18      bit_1.1-14         jsonlite_1.6       memoise_1.1.0      nlme_3.1-137       lattice_0.20-38   
[15] mgcv_1.8-26        Matrix_1.2-15      RNifti_0.10.0      DBI_1.0.0          oro.nifti_0.9.1    yaml_2.2.0         htmlwidgets_1.3   
[22] bit64_0.9-7        grid_3.5.2         neurobase_1.27.6   R6_2.4.0           blob_1.1.1         magrittr_1.5       matrixStats_0.54.0
[29] promises_1.0.1     htmltools_0.3.6    splines_3.5.2      abind_1.4-5        assertthat_0.2.1   mime_0.6           xtable_1.8-3      
[36] httpuv_1.4.5.1     R.oo_1.22.0       
> 

[muschellij2]

papayaWidget on GitHub is 0.5.5 - please reinstall and retry: remotes::install_github("muschellij2/papayaWidget")

John

On Wed, Jul 24, 2019 at 4:31 PM robertoromor notifications@github.com wrote:

session info below. Whay do you mean by "any example code"

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale: [1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252 LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Mexico.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] papayaWidget_0.5.4 WhiteStripe_2.3.1 shiny_1.2.0 RSQLite_2.1.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.0 compiler_3.5.2 later_0.8.0 R.methodsS3_1.7.1 bitops_1.0-6 base64enc_0.1-3 R.utils_2.8.0 [8] tools_3.5.2 digest_0.6.18 bit_1.1-14 jsonlite_1.6 memoise_1.1.0 nlme_3.1-137 lattice_0.20-38 [15] mgcv_1.8-26 Matrix_1.2-15 RNifti_0.10.0 DBI_1.0.0 oro.nifti_0.9.1 yaml_2.2.0 htmlwidgets_1.3 [22] bit64_0.9-7 grid_3.5.2 neurobase_1.27.6 R6_2.4.0 blob_1.1.1 magrittr_1.5 matrixStats_0.54.0 [29] promises_1.0.1 htmltools_0.3.6 splines_3.5.2 abind_1.4-5 assertthat_0.2.1 mime_0.6 xtable_1.8-3 [36] httpuv_1.4.5.1 R.oo_1.22.0

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[robertoromor]

rock and roll!! works perfectly, the update did it for me Thanks a lot John!