sce colnames missing: Error in [.data.table(sc1meta, , c("sampleID", as.character(sc1conf$ID)) column(s) not found: sampleID

[NadineBestard]

The issue #12 solved that the lack of colnames in the dimensional reduction causing errors in the app.
The lack of column names in the sce ( the cell names) also causes problems.
This hapens if the cell names of the single cell object are not defined ( the default for DropletUtils::read10xCounts)

> colnames(sce)
NULL

This is an issue that also caused the as.Seurat function to fail, as seen here and here.
The error that comes up in this case is:
Error in [.data.table(sc1meta, , c("sampleID", as.character(sc1conf$ID)) column(s) not found: sampleID

[jfouyang]

Can I clarify one thing? Which function gave the error message? Is it createConfig() or makeShinyApp()? It would be really helpful to know the exact function so as to speed up the troubleshooting process.

[NadineBestard]

sorry I forgot to mention that. it is the makeShinyApp() function.

[jfouyang]

Hi, first of all, apologies for the late reply. It has been a crazily hectic week for me.

I just checked and the absence of colnames in a SCE object does cause ShinyCell not to work propely. To circumvent that, I added an additional check to check if the colnames are present. And if they are not, the colnames will be populated with "cell_X" labels. I tested it on my end and everything works now. You can reinstall the latest version of shinycell to see if it works for your SCE object.

[NadineBestard]

Hi,
Don't worry, as I could detect from where the issue was comming from, it was easy to modify my object to add colnames and this was not holding me back! I just thought you would like to be aware of the problem and add something in your code like you did, to make it more robust to this comon situation for sce objects.
Many thanks for keeping improving this package!