check_spe() considerations

[jvelezmagic]

Hi Leo. Meeting Comments:

1. check_spe() should consider the requested assaynames and not default ones.
2. Probably barcode is now in colData and not in spatialData.
3. Describe the request to have the key column as a requirement.
4. Describe the special columns gene_id,gene_name, and gene_search.
5. Describe how to define the Layer column (e.g. filled of "NA").

[jvelezmagic]

Suggestions from today's meeting:

• Include generalization of labels (e.g., discrete variables, continuous variables).
• Generalization of special variables (e.g., SPATIALLIBD, logcounts).
• Notes for the user about the min_count parameter.
• Personal note: Reduced dimensions must have only the first two dimensions.

[lcolladotor]

• We no longer default to counts and logcounts and instead use the assayNames(spe).
• Barcode has been fixed.
• We describe key, gene_id, gene_name, gene_search in the new vignette.
• We changed Layer by ManualAnnotation and described in the vignette.
• We added a few help texts and changed the names of some of the main toggles. We also updated the documentation_spe.md file.
• We included a little help text box about the min count.
• At documentation_spe.md we mention that only the first 2 dimensions will be shown. The internal code can handle more dimensions now. Note that if no reduced dims are provided, the app will still work now.