tidySCE Speedup aggregate_cells

[stemangiola]

This has taken inspiration and motivation from

https://twitter.com/lcolladotor/status/1687475222687936512

[stemangiola]

Some discussion is here

Bioconductor/SummarizedExperiment#45

A proposal for a function is here

drisso/SingleCellExperiment#55

[stemangiola]

Data preparation

data(pbmc_small)
df <- pbmc_small
ids = df |> unite("id", factor, string) |> pull(id)

scuttle

microbenchmark(aggregateAcrossCells(df, ids), times = 10L, unit = "seconds")

Unit: seconds
                          expr       min        lq     mean    median        uq       max neval
 aggregateAcrossCells(df, ids) 0.1972021 0.2095963 0.214034 0.2129438 0.2222606 0.2374125    10

OLD tidySingleCellExperiment

microbenchmark(aggregate_cells(df, c(factor, string)), times = 10L)

Unit: seconds
                                   expr      min       lq    mean   median       uq     max neval
 aggregate_cells(df, c(factor, string)) 2.046285 2.106658 2.25975 2.129606 2.296099 2.88916    10

FIRST iteration 2x improvement b60f538

microbenchmark(aggregate_cells(df, c(factor, string)), times = 10L, unit = "second")
Unit: seconds
                                   expr       min        lq      mean    median        uq      max neval
 aggregate_cells(df, c(factor, string)) 0.9484644 0.9818873 0.9893115 0.9847042 0.9996955 1.063225    10

SECOND iteration 1/3x further improvement d302642

microbenchmark(aggregate_cells(df, c(factor, string)), times = 10L, unit = "second")
Unit: seconds
                                   expr       min        lq      mean    median        uq      max neval
 aggregate_cells(df, c(factor, string)) 0.6526753 0.6631348 0.7401931 0.6699366 0.6837512 1.064324    10

THIRD iteration 2x further improvement 4195aa8

microbenchmark(aggregate_cells(df, c(factor, string)), times = 10L, unit = "second")
Unit: seconds
                                   expr       min        lq      mean    median        uq      max neval
 aggregate_cells(df, c(factor, string)) 0.3838859 0.3932368 0.4351129 0.4167958 0.4408787 0.633195    10

FOURTH iteration 1.5x further improvement 5fb88fa

microbenchmark(aggregate_cells(df, c(factor, string)), times = 10L, unit = "second")
Unit: seconds
                                   expr       min        lq      mean    median        uq       max neval
 aggregate_cells(df, c(factor, string)) 0.2763835 0.2814492 0.2886746 0.2838345 0.2929347 0.3170838    10