datable is not rendered

[xtmgah]

Hello, Here is my app, i don't know why ggplot allplot1, allplot2, and table alltbl1 were not rendered, however, after remove (DT::dataTableOutput("alltbl1")) from UI, everything is fine. So, Could you check something wrong or it is a bug from DT or shiny. thanks.

library(shiny)
library(tidyverse)
library(ggrepel)

load("resultp.RData",envir=.GlobalEnv)
#save(,resultp_ratio_all_others,,resultp_normalization_all_others,resultp_normalization_uacc,resultp_ratio_uacc, resultp_normalization_hek,resultp_ratio_hek, file = "resultp.RData")

ui <- shinyUI(fluidPage(theme = "united",
                        navbarPage("MPRA analysis",
                                   tabPanel("MPRA Info",
                                            htmltools::includeHTML("info.html")
                                   ),
                                   tabPanel("ALL experiments",
                                            tabsetPanel(
                                              tabPanel("Ratio",
                                                       plotOutput("allplot1",height = 1000),
                                                       br(),
                                                       plotOutput("allplot2",height = 1000),
                                                       br(),
                                                       DT::dataTableOutput("alltbl1")),
                                              tabPanel("Normalization",
                                                       plotOutput("allplot3",height = 1000),
                                                       br(),
                                                       plotOutput("allplot4",height = 1000),
                                                       br()
                                              ),
                                              tabPanel("Others")
                                            )
                                   ),
                                   tabPanel("UACC903 Only"),
                                   tabPanel("HEK293FT Only")

                        )

))

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

  output$allplot1 <- renderPlot({
    datat3 <- resultp_ratio_all %>% filter(p.value< 10e-10 | abs(LFD)>log2(1.5))
    ggplot(resultp_ratio_all,aes(LFD,(-log10(p.value)),col=Color))+geom_point()+geom_vline(xintercept=c(-1,-2,1,2),linetype=2,col="gray80")+geom_hline(yintercept=c(2,3),linetype=2,col="gray80")+geom_text_repel(data=datat3,aes(label=Gene))+scale_color_manual("Significance",values = c("#e41a1c","#4daf4a","gray40"))+theme(legend.position="bottom", legend.box = "horizontal")
  },height = 1000)

  output$allplot2 <- renderPlot({
    datat3 <- resultp_ratio_all %>% filter(p.value< 10e-10 | abs(LFD)>log2(1.5))
    resultp_ratio_all %>% filter(p.value<0.05) %>% ggplot(aes(LFD,(log2(-log10(p.value))),col=Color))+geom_point()+geom_vline(xintercept=c(-1,-2,1,2),linetype=2,col="gray80")+geom_hline(yintercept=c(2,3),linetype=2,col="gray80")+geom_text_repel(data=datat3,aes(label=Gene))+scale_color_manual("Significance",values = c("#e41a1c","#4daf4a","gray40"))+theme(legend.position="bottom", legend.box = "horizontal")
  },height = 1000)

  output$alltbl1 <- DT::renderDataTable({
    resultp_ratio_all %>% select(-Color) %>% DT::datatable(filter = 'top',rownames = FALSE,extensions = 'Buttons', options = list(dom = 'Bfrtip', buttons = list('pageLength', 'csv', 'excel', 'pdf', 'print',list(extend = 'colvis')))) %>% DT::formatSignif(c(3:9,17:28), 5) %>% DT::formatStyle(c('p.value','p.adjust.BH','p.adjust.BY'), color = DT::styleInterval(c(0.01,0.05), c('red', 'purple', 'black'))) %>% DT::formatStyle('LFD', color = DT::styleInterval(c(-1,1), c('red', 'black', 'blue'))) %>% DT::formatStyle(c("totaltp_freq","wgs_freq"), color = DT::styleInterval(c(2,3), c('black', 'purple', 'red')))
  })

  output$allplot3 <- renderPlot({
    datat3 <- resultp_normalization_all %>% filter(p.value< 10e-10 | abs(LFD)>log2(1.5))
    ggplot(resultp_normalization_all,aes(LFD,(-log10(p.value)),col=Color))+geom_point()+geom_vline(xintercept=c(-1,-2,1,2),linetype=2,col="gray80")+geom_hline(yintercept=c(2,3),linetype=2,col="gray80")+geom_text_repel(data=datat3,aes(label=Gene))+scale_color_manual("Significance",values = c("#e41a1c","#4daf4a","gray40"))+theme(legend.position="bottom", legend.box = "horizontal")
  },height = 1000)

  output$allplot4 <- renderPlot({
    datat3 <- resultp_normalization_all %>% filter(p.value< 10e-10 | abs(LFD)>log2(1.5))
    resultp_normalization_all %>% filter(p.value<0.05) %>% ggplot(aes(LFD,(log2(-log10(p.value))),col=Color))+geom_point()+geom_vline(xintercept=c(-1,-2,1,2),linetype=2,col="gray80")+geom_hline(yintercept=c(2,3),linetype=2,col="gray80")+geom_text_repel(data=datat3,aes(label=Gene))+scale_color_manual("Significance",values = c("#e41a1c","#4daf4a","gray40"))+theme(legend.position="bottom", legend.box = "horizontal")
  },height = 1000)

})

# Run the application 
shinyApp(ui = ui, server = server)

#htmltools::tags$iframe(src = 'Promoter_GWAS_MPRA.html',frameborder="0", style="overflow: hidden; height: 100%; width: 100%; position: absolute;", height="100%", width="100%",scrolling="yes")

And here is my R session info:

> session_info()
Session info --------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.3.1 (2016-06-21)
 system   x86_64, darwin13.4.0        
 ui       RStudio (0.99.903)          
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            
 date     2016-10-10                  

Packages ------------------------------------------------------------------------------------
 package       * version date       source                           
 assertthat      0.1     2013-12-06 CRAN (R 3.3.0)                   
 BiocInstaller * 1.23.9  2016-09-04 Bioconductor                     
 colorspace      1.2-6   2015-03-11 CRAN (R 3.3.0)                   
 curl            2.1     2016-09-22 CRAN (R 3.3.0)                   
 DBI             0.5-1   2016-09-10 CRAN (R 3.3.0)                   
 devtools      * 1.12.0  2016-06-24 CRAN (R 3.3.0)                   
 digest          0.6.10  2016-08-02 CRAN (R 3.3.0)                   
 dplyr         * 0.5.0   2016-06-24 CRAN (R 3.3.0)                   
 DT            * 0.2     2016-08-09 CRAN (R 3.3.0)                   
 ggplot2       * 2.1.0   2016-03-01 CRAN (R 3.3.0)                   
 ggrepel       * 0.5     2016-02-08 CRAN (R 3.3.0)                   
 git2r           0.15.0  2016-05-11 CRAN (R 3.3.0)                   
 gtable          0.2.0   2016-02-26 CRAN (R 3.3.0)                   
 htmltools       0.3.5   2016-03-21 CRAN (R 3.3.0)                   
 htmlwidgets     0.7     2016-08-02 CRAN (R 3.3.1)                   
 httpuv          1.3.3   2015-08-04 CRAN (R 3.3.0)                   
 httr            1.2.1   2016-07-03 CRAN (R 3.3.0)                   
 jsonlite      * 1.1     2016-09-14 CRAN (R 3.3.0)                   
 labeling        0.3     2014-08-23 CRAN (R 3.3.0)                   
 lazyeval        0.2.0   2016-06-12 CRAN (R 3.3.0)                   
 magrittr        1.5     2014-11-22 CRAN (R 3.3.0)                   
 memoise         1.0.0   2016-01-29 CRAN (R 3.3.0)                   
 mime            0.5     2016-07-07 CRAN (R 3.3.0)                   
 munsell         0.4.3   2016-02-13 CRAN (R 3.3.0)                   
 plyr            1.8.4   2016-06-08 CRAN (R 3.3.0)                   
 purrr         * 0.2.2   2016-06-18 cran (@0.2.2)                    
 R.methodsS3     1.7.1   2016-02-16 CRAN (R 3.3.0)                   
 R.oo            1.20.0  2016-02-17 CRAN (R 3.3.0)                   
 R6              2.2.0   2016-10-05 CRAN (R 3.3.0)                   
 Rcpp            0.12.7  2016-09-05 CRAN (R 3.3.0)                   
 readr         * 1.0.0   2016-08-03 CRAN (R 3.3.0)                   
 rsconnect       0.4.3   2016-05-02 CRAN (R 3.3.0)                   
 scales          0.4.0   2016-02-26 CRAN (R 3.3.0)                   
 shiny         * 0.14.1  2016-10-10 Github (rstudio/shiny@c8a742a)   
 sourcetools     0.1.5   2016-09-15 CRAN (R 3.3.0)                   
 tibble        * 1.2     2016-08-26 cran (@1.2)                      
 tidyr         * 0.6.0   2016-08-12 CRAN (R 3.3.0)                   
 tidyverse     * 1.0.0   2016-09-26 Github (hadley/tidyverse@6e98d31)
 withr           1.0.2   2016-06-20 CRAN (R 3.3.0)                   
 xtable          1.8-2   2016-02-05 CRAN (R 3.3.0)                   
 yaml            2.1.13  2014-06-12 CRAN (R 3.3.0)                   
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] shiny_0.14.1         devtools_1.12.0      jsonlite_1.1         DT_0.2              
 [5] ggrepel_0.5          dplyr_0.5.0          purrr_0.2.2          readr_1.0.0         
 [9] tidyr_0.6.0          tibble_1.2           ggplot2_2.1.0        tidyverse_1.0.0     
[13] BiocInstaller_1.23.9

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7       git2r_0.15.0      plyr_1.8.4        R.methodsS3_1.7.1
 [5] tools_3.3.1       digest_0.6.10     memoise_1.0.0     gtable_0.2.0     
 [9] rstudioapi_0.6    DBI_0.5-1         curl_2.1          yaml_2.1.13      
[13] httr_1.2.1        withr_1.0.2       htmlwidgets_0.7   sourcetools_0.1.5
[17] grid_3.3.1        R6_2.2.0          magrittr_1.5      scales_0.4.0     
[21] htmltools_0.3.5   rsconnect_0.4.3   assertthat_0.1    mime_0.5         
[25] xtable_1.8-2      colorspace_1.2-6  httpuv_1.3.3      labeling_0.3     
[29] lazyeval_0.2.0    munsell_0.4.3     R.oo_1.20.0      

[wch]

Can you provide a minimal reproducible example? This means something that we would be able to run and test.

[xtmgah]

Hello:

Here is the minimal test. I think the app will working only excluded "htmltools::includeHTML("info.html")". Once it included, the figure and table will not rendered. Check it and let me know how to solve it. thanks.

test.zip

[wch]

I believe the problem is that the info.html file that you are including is a complete document, with its own and embedded scripts, which conflict with the ones that Shiny puts in the generated webpage. If you comment out the includeHTML("info.html"), everything else works.

You'll need to clean up the info.html file so that it's not a complete HTML document, but one that just has the content that needs to be embedded, or not embed the .html file at all.

[xtmgah]

OK. that what i am guessing. So, Is there any simple way to clean html files?

[wch]

You'll have to open it in a text editor and remove all the extra stuff.

[xtmgah]

Thanks.