Labels disappear in Rmd "Show in New Window"

[gregleleu]

Summary

I use Rmd notebooks in R studio, with plots displayed in the chunk output. Rstudio lets you open these outputs in a new window (e.g. to have a bigger view). When opening a new window with the plot labels disappear, I guess they are not redrawn?

Version information

Using ggrepel 0.8.0.9C, but it's been like that for ever.

Here is the output from sessionInfo() in my R session:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] ggraph_1.0.2       igraph_1.2.2       ggmosaic_0.2.0     leaflet_2.0.2      sf_0.7-1           future.apply_1.0.1 bindrcpp_0.2.2    
 [8] rvest_0.3.2        xml2_1.2.0         furrr_0.1.0        future_1.10.0      magrittr_1.5       forcats_0.3.0      stringr_1.3.1     
[15] dplyr_0.7.7        purrr_0.2.5        readr_1.1.1        tidyr_0.8.2        tibble_1.4.2       ggplot2_3.1.0      tidyverse_1.2.1   

loaded via a namespace (and not attached):
  [1] utf8_1.1.4          proto_1.0.0         tidyselect_0.2.5    lme4_1.1-18-1       RSQLite_2.1.1       htmlwidgets_1.3    
  [7] grid_3.5.1          munsell_0.5.0       codetools_0.2-15    units_0.6-1         chron_2.3-53        smbinning_0.7      
 [13] withr_2.1.2         colorspace_1.3-2    knitr_1.20          rstudioapi_0.8      stats4_3.5.1        ROCR_1.0-7         
 [19] TTR_0.23-4          listenv_0.7.0       labeling_0.3        rstan_2.18.2        urltools_1.7.1      farver_1.0         
 [25] bit64_0.9-7         rprojroot_1.3-2     xfun_0.4            ggthemes_4.0.1      productplots_0.1.1  R6_2.3.0           
 [31] dlookr_0.3.2        bitops_1.0-6        assertthat_0.2.0    promises_1.0.1      networkD3_0.4       scales_1.0.0       
 [37] nnet_7.3-12         debugme_1.1.0       gtable_0.2.0        globals_0.12.4      processx_3.2.0      sandwich_2.5-0     
 [43] rlang_0.3.0.1       splines_3.5.1       lazyeval_0.2.1      acepack_1.4.1       inline_0.3.15       mapview_2.6.0      
 [49] broom_0.5.0         checkmate_1.8.5     yaml_2.2.0          reshape2_1.4.3      abind_1.4-5         modelr_0.1.2       
 [55] crosstalk_1.0.0     backports_1.1.2     httpuv_1.4.5        quantmod_0.4-13     Hmisc_4.1-1         rmapshaper_0.4.1   
 [61] inum_1.0-0          tools_3.5.1         tcltk_3.5.1         spData_0.2.9.4      gplots_3.0.1        kableExtra_0.9.0   
 [67] raster_2.8-4        RColorBrewer_1.1-2  jsonvalidate_1.0.0  gsubfn_0.7          Rcpp_1.0.0          plyr_1.8.4         
 [73] base64enc_0.1-3     classInt_0.2-3      prettyunits_1.0.2   ps_1.2.1            rpart_4.1-13        sqldf_0.4-11       
 [79] viridis_0.5.1       zoo_1.8-4           ggrepel_0.8.0.9000  haven_1.1.2         cluster_2.0.7-1     fs_1.2.6           
 [85] tinytex_0.9         DataExplorer_0.7.0  data.table_1.11.8   magick_2.0          openxlsx_4.1.0      triebeard_0.3.0    
 [91] mvtnorm_1.0-8       mitml_0.3-6         htmltidy_0.4.0      matrixStats_0.54.0  hms_0.4.2           RcmdrMisc_2.5-1    
 [97] mime_0.6            evaluate_0.12       xtable_1.8-3        XML_3.98-1.16       DMwR_0.4.1          rio_0.5.10         
[103] readxl_1.1.0.9000   gridExtra_2.3       compiler_3.5.1      mice_3.3.0          KernSmooth_2.23-15  V8_1.5             
[109] crayon_1.3.4        StanHeaders_2.18.0  minqa_1.2.4         htmltools_0.3.6     later_0.7.5         Formula_1.2-3      
[115] libcoin_1.0-1       lubridate_1.7.4     DBI_1.0.0           tweenr_1.0.0        corrplot_0.84       MASS_7.3-51.1      
[121] Matrix_1.2-15       car_3.0-2           cli_1.0.1           gdata_2.18.0        parallel_3.5.1      bindr_0.1.1        
[127] pan_1.6             pkgconfig_2.0.2     prettydoc_0.2.1     foreign_0.8-71      sp_1.3-1            plotly_4.8.0       
[133] geojsonlint_0.2.0   webshot_0.5.1       callr_3.0.0         digest_0.6.18       janitor_1.1.1       rmarkdown_1.10     
[139] cellranger_1.1.0    htmlTable_1.12      nortest_1.0-4       curl_3.2            shiny_1.2.0         gtools_3.8.1       
[145] satellite_1.0.1     jomo_2.6-4          nloptr_1.2.1        nlme_3.1-137        jsonlite_1.5        carData_3.0-2      
[151] fansi_0.4.0         viridisLite_0.3.0   pillar_1.3.0        loo_2.0.0           lattice_0.20-38     pkgbuild_1.0.2     
[157] httr_1.3.1          survival_2.43-1     glue_1.3.0          xts_0.11-2          zip_1.0.0           png_0.1-7          
[163] bit_1.1-14          ggforce_0.1.3       class_7.3-14        stringi_1.2.4       blob_1.1.1          moments_0.14       
[169] partykit_1.2-2      latticeExtra_0.6-28 caTools_1.17.1.1    memoise_1.1.0       styler_1.0.2        e1071_1.7-0     

[slowkow]

Hi Greg, thanks for describing your issue.

I'm still a bit hazy on exactly what you're experiencing. I don't think I could reproduce this issue myself based on your description.

Could I ask you to please break it down into a set of steps, ideally with a minimal snippet of code that I can run in my own RStudio? I'd like to follow along and see if I get the same behavior on my machine.

Thanks!

[gregleleu]

Sure,

Super simple example:

library(ggplot2)
library(ggrepel)
library(dplyr)

ggdata <- diamonds %>% 
  group_by(cut) %>% 
  summarise_at(vars(depth, table), mean)

ggdata %>% 
  ggplot() +
  geom_point(aes(x = depth, y = table)) +
  geom_text_repel(aes(x = depth, y = table, label = cut))

Works fine in the normal chunk output:

But completely disappears in the new window (I think they're called satellite windows):

In latest Rstudio daily (1.2.1114) but it's been like that always. Session info:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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] dplyr_0.7.8        ggrepel_0.8.0.9000 ggplot2_3.1.0     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       rstudioapi_0.8   knitr_1.20       bindr_0.1.1      magrittr_1.5     tidyselect_0.2.5
 [7] munsell_0.5.0    colorspace_1.3-2 R6_2.3.0         rlang_0.3.0.1    plyr_1.8.4       tools_3.5.1     
[13] grid_3.5.1       gtable_0.2.0     withr_2.1.2      lazyeval_0.2.1   assertthat_0.2.0 tibble_1.4.2    
[19] crayon_1.3.4     bindrcpp_0.2.2   purrr_0.2.5      glue_1.3.0       labeling_0.3     compiler_3.5.1  
[25] pillar_1.3.0     scales_1.0.0     pkgconfig_2.0.2 

[joshbiology]

I am seeing this issue as well. For me, the redraw occurs after I restart my RStudio session and open up an old RMD. All the ggrepel labels will be gone from my plots.

[SebastianHesse]

I have the same issue woking with mark-down. The ggrepel labels are shown correctly in the graphic directly implemented in the markdown script but when I click "show in new window" at the upper right side off the graph (eg to look at it a bigger size), the labels disappear.

[slowkow]

I was able to reproduce the issue on my laptop:

https://vimeo.com/318265708#t=52s

It seems everything works as expected, except for Show in New Window

We should contact RStudio developers and ask if they have any ideas about why this is happening.

[slowkow]

It seems this is a bug in RStudio, not ggrepel.