App crashes using seurat object as dataset

[Michael-Geuenich]

I've tried uploading the scRNAseq_longitudinal_LCMV_Arm_Cl13.Rds dataset from here: https://www.dropbox.com/sh/0b0zb0xd6ycxn0y/AAAQsL0yZ9kfAcOmwodN4QhFa?dl=0

The app crashes before I can select any assay or cell type column with the following error:

Listening on http://127.0.0.1:5117
Warning: Error in <Anonymous>: unable to find an inherited method for function ‘assays’ for signature ‘"character"’
  3: runApp
  2: print.shiny.appobj
  1: <Anonymous>

This might be an issue with the functions in sccwiz though

[matt-sd-watson]

For this object is looks like all of the gene names are lowercase:

head(rownames(long_sce))

Mrpl15 Lypla1 Gm37988 Tcea1 Atp6v1h Rb1cc1

so likely the gene parsing functions are returning no hits from annotables. We may want to build in a check for capitalization of gene symbols.

when i convert the row names to uppercase it is able to run.

[kieranrcampbell]

lower case is almost always mouse, is this dataset definitely human?

[Michael-Geuenich]

Oh, good point. This is a mouse dataset - I just forgot that we don't support mouse yet

[kieranrcampbell]

can we add functionality that throws an error if the genes are lowercase? ("Looks like your dataset is mouse but we don't support this yet")