Additional TO DO items

[jeremymiller]

• [ ] Add a verbose tag to mapping to avoid printing out all the output from tree and especially hierarchical mapping.
• [ ] Make the off-target selection and subsetting components of buildPatchseqTaxonomy less complicated (e.g., for subsetting, just provide a vector, and all the relevant things in the uns are also updated).
• [ ] Remove all the stuff about taxonomy directories and taxonomy mode directories for buildPatchseqTaxonomy, as they are not needed
• [ ] Allow for a cell x gene matrix with cells as ROWS to be provided (taxonomy) <- Jeremy already updated cpm/logCPM for this, but nothing else
• [ ] Provide default method for variable gene calculation in buildTaxonomy and buildPatchseqTaxonomy
• [ ] Variable genes are not selected during buildPatchseqTaxonomy <-- which genes are used for correlation mapping in this case? It looks like it's the general variable genes, but really we should be using mode-specific genes. So we should switch AIT.anndata$var$highly_variable_genes to something like AIT.anndata$var$highly_variablegenes[MODE]

[UCDNJJ]

Agreed variable genes should be associated with a mode. We should be consistent and do something like AIT.anndata$uns$corr$mode$highly_variable_genes.