Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
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neilzhao ▴ 30
@0f8d7a2e
Last seen 12 days ago
United States

My apologies if this is a naïve question, is it possible to host the cytoviewer <shiny.appobj> class instance of a list, with nested ui and server components, to shinyapps.io or Posit connect/cloud?

Our images, masks, and cell-level metadata for the CytoImageList and SingleCellExperiment objects contain sensitive information. And unfortunately our collaborators don't use R, but would greatly benefit from the interactive visualization and exploration of multi-channel images and segmentation masks hosted remotely on a Shiny server URL.

For example, in the tutorial Bioconductor html vignette, the app is the <shiny.appobj> class instance of a list that I would like to privately share and deploy with our custom data:

library(cytoviewer)
library(cytomapper)

# Load example datasets 
data("pancreasImages")
data("pancreasMasks")
data("pancreasSCE")

# Use cytoviewer with images, masks and object
app <- cytoviewer(image = pancreasImages, 
                  mask = pancreasMasks, 
                  object = pancreasSCE, 
                  img_id = "ImageNb", 
                  cell_id = "CellNb")

if (interactive()) {

  shiny::runApp(app)

  }

Any suggestions? Thank you!

Here is my sessioninfo:
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rsconnect_1.2.2             BiocStyle_2.26.0            shiny_1.8.1.1               cytomapper_1.10.1          
 [5] EBImage_4.40.1              cytoviewer_1.3.3            pivottabler_1.5.5           zeallot_0.1.0              
 [9] reshape2_1.4.4              spdep_1.3-3                 sf_1.0-16                   spData_2.3.0               
[13] Rmixmod_2.1.10              Rcpp_1.0.12                 stringdist_0.9.12           fuzzyjoin_0.1.6            
[17] lubridate_1.9.3             forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                
[21] purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
[25] ggplot2_3.5.1               tidyverse_2.0.0             readxl_1.4.3                future.apply_1.11.2        
[29] future_1.33.2               CELESTA_0.0.0.9000          SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
[33] Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0             
[37] S4Vectors_0.36.2            BiocGenerics_0.44.0         MatrixGenerics_1.10.0       matrixStats_1.2.0          

loaded via a namespace (and not attached):
  [1] utf8_1.2.4                shinydashboard_0.7.2      R.utils_2.12.3            tidyselect_1.2.1          htmlwidgets_1.6.4        
  [6] grid_4.2.1                BiocParallel_1.32.6       DropletUtils_1.18.1       munsell_0.5.1             codetools_0.2-19         
 [11] ragg_1.3.1                units_0.8-5               miniUI_0.1.1.1            withr_3.0.0               colorspace_2.1-0         
 [16] knitr_1.46                rstudioapi_0.16.0         wk_0.9.1                  listenv_0.9.1             GenomeInfoDbData_1.2.9   
 [21] rhdf5_2.42.1              parallelly_1.37.1         vctrs_0.6.5               generics_0.1.3            xfun_0.43                
 [26] timechange_0.3.0          R6_2.5.1                  ggbeeswarm_0.7.2          locfit_1.5-9.9            bitops_1.0-7             
 [31] rhdf5filters_1.10.1       cachem_1.0.8              DelayedArray_0.24.0       promises_1.2.1            shinycssloaders_1.0.0    
 [36] scales_1.3.0              beeswarm_0.4.0            gtable_0.3.5              beachmat_2.14.2           globals_0.16.3           
 [41] rlang_1.1.1               systemfonts_1.0.5         BiocManager_1.30.23       s2_1.1.6                  yaml_2.3.8               
 [46] abind_1.4-5               httpuv_1.6.14             tools_4.2.1               bookdown_0.39             SpatialExperiment_1.8.1  
 [51] raster_3.6-26             jquerylib_0.1.4           RColorBrewer_1.1-3        proxy_0.4-27              plyr_1.8.9               
 [56] sparseMatrixStats_1.10.0  zlibbioc_1.44.0           classInt_0.4-10           RCurl_1.98-1.14           openssl_2.1.2            
 [61] deldir_2.0-2              viridis_0.6.5             fontawesome_0.5.2         magrittr_2.0.3            data.table_1.15.0        
 [66] magick_2.8.3              colourpicker_1.3.0        hms_1.1.3                 mime_0.12                 fftwtools_0.9-11         
 [71] evaluate_0.23             archive_1.1.8             xtable_1.8-4              jpeg_0.1-10               gridExtra_2.3            
 [76] compiler_4.2.1            KernSmooth_2.23-22        crayon_1.5.2              R.oo_1.26.0               htmltools_0.5.8.1        
 [81] later_1.3.2               tzdb_0.4.0                tiff_0.1-12               DBI_1.2.2                 boot_1.3-28.1            
 [86] Matrix_1.6-5              cli_3.6.1                 R.methodsS3_1.8.2         parallel_4.2.1            pkgconfig_2.0.3          
 [91] sp_2.1-3                  terra_1.7-71              scuttle_1.8.4             svglite_2.1.3             vipor_0.4.7              
 [96] bslib_0.7.0               dqrng_0.3.2               XVector_0.38.0            digest_0.6.32             rmarkdown_2.26           
[101] cellranger_1.1.0          edgeR_3.40.2              DelayedMatrixStats_1.20.0 curl_5.2.1                rjson_0.2.21             
[106] lifecycle_1.0.4           jsonlite_1.8.8            Rhdf5lib_1.20.0           viridisLite_0.4.2         askpass_1.2.0            
[111] limma_3.54.2              fansi_1.0.6               pillar_1.9.0              lattice_0.22-5            fastmap_1.1.1            
[116] glue_1.6.2                png_0.1-8                 svgPanZoom_0.3.4          class_7.3-22              stringi_1.8.3            
[121] sass_0.4.9                HDF5Array_1.26.0          nnls_1.5                  textshaping_0.3.7         memoise_2.0.1            
[126] e1071_1.7-14             
cytoviewer ShinyApps • 95 views
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