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