Add info useful for the shiny app

[lcolladotor]

From https://github.com/LieberInstitute/spatialLIBD/blob/002838163e6373f4d3899f74fd867c6c6fe91eab/inst/scripts/make-data_spatialLIBD.R add some useful information such as:

• the chrM columns https://github.com/LieberInstitute/spatialLIBD/blob/002838163e6373f4d3899f74fd867c6c6fe91eab/inst/scripts/make-data_spatialLIBD.R#L63-L66
• rowData(sce)$gene_search which combines the gene symbol and the Ensembl gene ID as in https://github.com/LieberInstitute/spatialLIBD/blob/002838163e6373f4d3899f74fd867c6c6fe91eab/inst/scripts/make-data_spatialLIBD.R#L106-L108

At this point, you could use spatialLIBD::check_sce() and see what else is missing http://research.libd.org/spatialLIBD/reference/check_sce.html.

[lcolladotor]

Also add the key like in https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/sce_scran.R#L245 which we'll use for plotting the data with plotly.

[abspangler13]

output of check_sce() tells us we must turn rownames(sce) into rowData(sce)$gene_id

[bpardo99]

From this issue we are just missing this:

• We have to re-run spatialLIBD::check_sce() when we add things on issue Add reduced dimensions #10 and Add number of cells per spot #11

[lcolladotor]

We now have to implement a spatialLIBD::check_spe(), however, I think that this issue is mostly done.

Related to https://github.com/LieberInstitute/spatialDLPFC/blob/main/analysis/01_build_SPE.R#L488-L489

[lcolladotor]

Note for Leo: create an issue on spatialLIBD with details for Brenda so we can make check_spe()