Help using ShinyCell2 and Seurat v5 object.

Question

[Jamie]

Hello! Currently I am trying to create a shinycell app with my seurat object. However, I keep on encountering this error:

Error in sc1gexpr.grp$create_dataset("data", dtype = h5types$H5T_NATIVE_FLOAT, : The length of the chunk_dims is 1 and has to be the same as the rank of the space 0

What does this error mean? My seurat object was created with seurat v5, and I ran SCTransform and integration already. I am currently trying to use ShinyCell2.

Here is my entire code:

library(Seurat)
library(ShinyCell2)

seu <- readRDS("/Users/jamiechoe/Desktop/PracticeRNA/jamie_project/Merged_Donors/Merged_Donors.rds")

scConf <- createConfig(seu)

makeShinyApp(seu, scConf, gene.mapping = TRUE, gex.assay = "SCT", shiny.title = "All Cells Shiny App", shiny.dir = "/Users/jamiechoe/Desktop/PracticeRNA/jamie_project/shinyApp")

scConf <- createConfig(seu)
makeShinyFiles(seu,scConf, shiny.prefix="sc1", shiny.dir="shinyApp/")
makeShinyCodes(shiny.title = "PBMC multiomics", shiny.prefix="sc1",
               shiny.dir="shinyApp/")

How could I go about fixing this error?

Thank you so much!

[antonioggsousa]

I never used this ShinyApp, but are you sure you can provide SCT assays? According to the documentation of makeShinyFiles you must provide one of the following assays: RNA or integrated (see: https://github.com/the-ouyang-lab/ShinyCell2/blob/main/R/makeShinyFiles.R#L12).