Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
0
0
Entering edit mode
neilzhao ▴ 30
@0f8d7a2e
Last seen 3 months 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 • 218 views
ADD COMMENT

Login before adding your answer.

Traffic: 624 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6