Improve the stability of the knee point identification.

[LTLA]

Closes #115.

[LTLA]

Looks good for the suite of test datasets in DropletTestFiles.

library(DropletTestFiles)
X <- listTestFiles()
keep <- grep("Raw HDF5", X$description)

png("results.png", width=6, height=10, units="in", res=120)
library(DropletUtils)
par(mfrow=c(3,2))
for (i in keep) {
    path <- getTestFile(X$rdatapath[i], prefix=FALSE)
    se <- read10xCounts(path, type="HDF5")
    current <- barcodeRanks(assay(se))
    o <- order(current$rank)
    plot(current$rank[o], current$total[o], log="xy", type="l", main=X$file.dataset[i])
    abline(h=metadata(current)$knee, lty=2)
    abline(h=metadata(current)$inflection, lty=3)
}
dev.off()

Session information

R Under development (unstable) (2024-10-30 r87277)
Platform: aarch64-apple-darwin22.6.0
Running under: macOS Ventura 13.7

Matrix products: default
BLAS:   /Users/luna/Software/R/trunk/lib/libRblas.dylib
LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] DropletUtils_1.25.2         SingleCellExperiment_1.29.1
 [3] SummarizedExperiment_1.37.0 Biobase_2.67.0
 [5] GenomicRanges_1.59.1        GenomeInfoDb_1.43.2
 [7] IRanges_2.41.1              S4Vectors_0.45.2
 [9] BiocGenerics_0.53.3         generics_0.1.3
[11] MatrixGenerics_1.19.0       matrixStats_1.4.1
[13] DropletTestFiles_1.17.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1          dplyr_1.1.4
 [3] blob_1.2.4                filelock_1.0.3
 [5] R.utils_2.12.3            Biostrings_2.75.1
 [7] fastmap_1.2.0             BiocFileCache_2.15.0
 [9] mime_0.12                 lifecycle_1.0.4
[11] statmod_1.5.0             KEGGREST_1.47.0
[13] RSQLite_2.3.9             magrittr_2.0.3
[15] compiler_4.5.0            rlang_1.1.4
[17] tools_4.5.0               utf8_1.2.4
[19] yaml_2.3.10               S4Arrays_1.7.1
[21] dqrng_0.4.1               bit_4.5.0.1
[23] curl_6.0.1                DelayedArray_0.33.3
[25] abind_1.4-8               BiocParallel_1.41.0
[27] HDF5Array_1.35.2          withr_3.0.2
[29] purrr_1.0.2               R.oo_1.27.0
[31] grid_4.5.0                fansi_1.0.6
[33] ExperimentHub_2.15.0      beachmat_2.23.3
[35] Rhdf5lib_1.29.0           edgeR_4.5.1
[37] cli_3.6.3                 crayon_1.5.3
[39] httr_1.4.7                DelayedMatrixStats_1.29.0
[41] scuttle_1.17.0            DBI_1.2.3
[43] cachem_1.1.0              rhdf5_2.51.0
[45] zlibbioc_1.53.0           parallel_4.5.0
[47] AnnotationDbi_1.69.0      BiocManager_1.30.25
[49] XVector_0.47.0            vctrs_0.6.5
[51] Matrix_1.7-1              jsonlite_1.8.9
[53] bit64_4.5.2               locfit_1.5-9.10
[55] limma_3.63.2              glue_1.8.0
[57] codetools_0.2-20          BiocVersion_3.21.1
[59] UCSC.utils_1.3.0          tibble_3.2.1
[61] pillar_1.9.0              rappdirs_0.3.3
[63] rhdf5filters_1.19.0       GenomeInfoDbData_1.2.13
[65] R6_2.5.1                  dbplyr_2.5.0
[67] sparseMatrixStats_1.19.0  lattice_0.22-6
[69] AnnotationHub_3.15.0      png_0.1-8
[71] R.methodsS3_1.8.2         memoise_2.0.1
[73] Rcpp_1.0.13-1             SparseArray_1.7.2
[75] pkgconfig_2.0.3