updated documentation and assay utilization

[ncborcherding]

This is mostly to get around Seurat complete deprecation of slot leading to the error:

creating vignettes ... ERROR
--- re-building ‘escape.Rmd’ using rmarkdown

Quitting from escape.Rmd:188-200 [unnamed-chunk-10]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/lifecycle_error_deprecated>
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
  5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
---
Backtrace:
    ▆
 1. └─escape::escape.matrix(...)
 2.   └─escape:::.cntEval(input.data, assay = "RNA", type = "counts")
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─SeuratObject::GetAssayData(obj, assay = assay, slot = type)
 6.     └─SeuratObject:::GetAssayData.Seurat(obj, assay = assay, slot = type)
 7.       └─SeuratObject::.Deprecate(...)
 8.         └─lifecycle::deprecate_stop(...)
 9.           └─lifecycle:::deprecate_stop0(msg)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'escape.Rmd' failed with diagnostics:
The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.

While at it - I fixed the documentation to be consistent.

[codecov]

Codecov Report

❌ Patch coverage is 90.43478% with 11 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/utils.R	88.13%	7 Missing ⚠️
R/geyserEnrichment.R	69.23%	4 Missing ⚠️

Files with missing lines	Coverage Δ
R/densityEnrichment.R	98.46% <100.00%> (+0.04%)	⬆️
R/enrichIt.R	92.72% <ø> (ø)
R/enrichItPlot.R	92.64% <100.00%> (ø)
R/getGeneSets.R	69.38% <ø> (ø)
R/gseaEnrichment.R	91.26% <100.00%> (ø)
R/heatmapEnrichment.R	98.00% <100.00%> (ø)
R/pcaEnrichment.R	91.80% <100.00%> (ø)
R/performNormalization.R	75.55% <ø> (ø)
R/performPCA.R	83.33% <ø> (ø)
R/ridgeEnrichment.R	94.73% <100.00%> (ø)
... and 5 more

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