Add variables to explore low quality spots from scran

[lcolladotor]

Before #8 and likely also before #7, we'll want to add a few things to our sce object. One of them could be a (or more than one) discrete variable https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L58 that tells us what were spots that scran's quality control checks (designed for scRNA-seq data, not Visium data) are of low quality and should be discarded. That is, running code like https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/sce_scran.R#L32-L33 then taking the outputs (which are logical vectors) and converting them to discrete variables (so factor or character).

Let's try this with the 3 columns in https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/sce_scran.R#L35. So something like:

sce$scran_discard <- factor(edit_me, levels = c("TRUE", "FALSE"))
sce$scran_low_lib_size <- ...
sce$low_n_features <- ...

This might be more relevant for the LC data than the DLPFC data. But it'll be good to check.