"data" slot not found

[swarnalidasgupta]

Hello,

I wanted to generate shinycell objects from my seurat object, but the function is unable to find the data slot in the gex.slot = "data" input, maybe because seurat v5 does not store counts, data and scaled.data as slots anymore, instead it stores it as layers. How can I still generate my shinycell objects?

[olneykimberly]

I am having the same issue, but data slot is in my object

> makeShinyApp(obj = dataObject.annotated,
+              scConf = sc.config, 
+             # gene.mapping = TRUE,
+              shiny.dir = paste0("../../shiny_apps/shiny_", treatment),
+              shiny.title = paste0("10X"))
Error in slot(obj@assays[[gex.assay[1]]], gex.slot[1]) : 
  no slot of name "data" for this object of class "Assay5"

> Assays(dataObject.annotated)
An object of class "SimpleAssays"
Slot "data":
List of length 1

[swarnalidasgupta]

I am having the same issue, and I have the data slot in my object as well; somehow I am not able to access it using the Shiny function.

[monikaramos]

Has this been solved or can the shinycell package be updated so that we can use it on seurat v5 objects?

[tjakobi]

Hi everyone,

I just had the same issue right now.

There is already code in ShinyCell for v5 Seurat objects, however, the code is only 6 months old and not part of the 2.1 release (see commit 5ede118).

Installing the latest shinycell from GitHub solved the issues for me:

devtools::install_github("SGDDNB/ShinyCell")

Importantly, layers have to be joined before running makeShinyApp:

obj <- JoinLayers(obj)

[jiayongpengboy]

seu1 = UpdateSeuratObject(object = seu) #
scConf = createConfig(seu1)

makeShinyApp(seu1, scConf, gene.mapping = TRUE,
shiny.title = "ShinyCell Quick Start")

#run ok