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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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[BUG] Cannot resume manual annotation #40

Closed lcolladotor closed 2 years ago

lcolladotor commented 2 years ago

First reported by @Erik-D-Nelson at https://jhu-genomics.slack.com/archives/C03KD30V3ST/p1657043593610579

I was using R version 4.2.0, SpatialExperiment version 1.6.0, and spatialLIBD version 1.8.3. I think the latest version of R is 4.2.1 but I believe the package versions are current I'll try using this other Shiny app quickly and let you know what I find! Thanks! I went on the lymph node app (EDIT: https://libd.shinyapps.io/spatialLIBD_Human_Lymph_Node_10x/) and successfully generated this csv file: spatialLIBD_ManualAnnotation_2022-07-05_17-57-08.csv It's just two square regions of the tissue, annotated test1 or test2. After I made these, I closed the app and started a new session. When I try to upload the csv to the Shiny app, it doesn't seem to work, as all spots are categorized as NA and none as test1 or test2. So, I think this may be an bug with the current version of spatialLIBD or a dependency/dependencies and not the HPC app

lcolladotor commented 2 years ago

Local test where it works:

Screen Shot 2022-07-15 at 2 45 54 PM
lcolladotor commented 2 years ago

https://libd.shinyapps.io/spatialLIBD_Human_Lymph_Node_10x/ is now updated too