get_expressed_genes - fix for Seurat v5 and add method for matrices

[csangara]

In Seurat v4, the 'count' and 'data' slots are always present in the object - that is, a newly created Seurat object is initialized with both slots by default. This is not the case in Seurat v5, as objects are only initialized with the 'count' slot.

Since get_expressed_genes directly accesses the 'data' slot, this can cause errors in Seurat v5.

The following changes to the function has been implemented:

• Use GetAssayData to access the expression matrix -> this means we can remove specific checks for each assay (SCT, integrated, Spatial, ...) because checks will be done by Seurat
• Allow additional parameters to be passed to GetAssayData as ... (to handle difference in 'slot' and 'layer' terminology between versions)
• If no value for assay_oi is given, the DefaultAssay will be used instead of the most 'advanced' assay as previously done
• Turned the function into a generic and implemented a method for matrices (get_expressed_genes.default)
  • The order of arguments has changed from function(ident, seurat_obj, pct = 0.1, assay_oi = NULL) to function(seurat_obj, ident, assay_oi = NULL, pct = 0.1, ...) because the main object has to be the first argument

[codecov-commenter]

Codecov Report

Attention: 100 lines in your changes are missing coverage. Please review.

Comparison is base (0e14cbe) 70.08% compared to head (7d13d91) 69.59%.
Report is 14 commits behind head on master.

Files	Patch %	Lines
R/supporting_functions.R	26.19%	62 Missing ⚠️
R/application_prediction.R	42.42%	38 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #247      +/-   ##
==========================================
- Coverage   70.08%   69.59%   -0.50%     
==========================================
  Files          16       16              
  Lines        5419     5472      +53     
==========================================
+ Hits         3798     3808      +10     
- Misses       1621     1664      +43     

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[csangara]

Replaced by #250 - the function is rewritten to keep the argument ordering consistent.