edit scuttle to scrapper for aggregateAcrossCells()

[manishabarse]

We noticed that the package test was breaking [here] after the warning message:

Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.

The aggregateAcrossCells() function in the scuttle package is being phased out in favor of the new scrapper package ([scuttle issue #36](LTLA/scuttle#36 (comment))) and has also been replaced in recent Bioconductor updates, such as in imcRtools ([Bioconductor 3.23 Release]. Additionally, internal arguments such as average have been deprecated in favor of statistics link.

Implementation

The initial implementation directly replaced scuttle::aggregateAcrossCells() with scrapper::aggregateAcrossCells(). However, the two functions work differently.

scuttle::aggregateAcrossCells() accepts a SingleCellExperiment and returns a SingleCellExperiment, while the scrapper::aggregateAcrossCells() implementation currently available to us operates on a matrix-like input and returns a list containing the aggregated counts and grouping information (sums, detected, combinations, counts, and index).

Therefore, directly passing the SingleCellExperiment to scrapper::aggregateAcrossCells() resulted in:

Error in dim(x) <- length(x) : invalid first argument, must be vector (list or atomic)

The implementation was updated to aggregate the counts matrix with scrapper::aggregateAcrossCells() and reconstruct the SingleCellExperiment. The original colData is also reconstructed, preserving the original column types and retaining the grouping variables (registration_variable, registration_sample_id) and ncells, to reproduce the structure of the previous scuttle output.

Validation

The updated registration_pseudobulk() implementation was tested against the previous scuttle implementation using the same example. The resulting SingleCellExperiment objects are now identical using:

testthat::expect_identical(sce_pseudo, test_pseudo) and testthat::expect_equal(sce_pseudo, test_pseudo).

@Nick-Eagles and @lahuuki helped to test this.