The waddR package provides two testing procedures using
the 2-Wasserstein distance to test whether two distributions FA and FB given in the
form of samples are different by specifically testing the null
hypothesis H0 : FA = FB
against the alternative H1 : FA ≠ FB.
The first, semi-parametric (SP), procedure uses a test based on permutations combined with a generalized Pareto distribution approximation to estimate small p-values accurately.
The second procedure (ASY) uses a test based on asymptotic theory which is valid only if the samples can be assumed to come from continuous distributions.
To demonstrate the capabilities of the testing procedures, we consider models based on normal distributions here. We exemplarily construct three cases in which two distributions (samples) differ with respect to location, size, and shape, respectively, and one case without a difference. For convenience, we focus on the p-value, the value of the (squared) 2-Wasserstein distance, and the fractions of the location, size, and shape terms (in %) with respect to the (squared) 2-Wasserstein distance here, while the functions also provide additional output.
We start with an example, in which the two distributions (samples) are supposed to only differ with respect to the location, and show the results for the two testing procedures (SP and ASY).
Note that the semi-parametric method “SP” with a permutation number
of 10000 is used by default in wasserstein.test if nothing
else is specified. The permutation procedure in the “SP” method uses a
random group assignment step, and to obtain reproducible results, a seed
can be set from the user environment before calling
wasserstein.test.
set.seed(24)
ctrl<-rnorm(300,0,1)
dd1<-rnorm(300,1,1)
set.seed(32)
wasserstein.test(ctrl,dd1,method="SP",permnum=10000)[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.000000 1.162487 98.100000 0.070000 1.830000
wasserstein.test(ctrl,dd1,method="ASY")[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.000000 1.162487 98.100000 0.070000 1.830000We obtain a very low p-value, clearly pointing at the existence of a difference, and see that differences with respect to location make up by far the major part of the 2-Wasserstein distance.
Analogously, we look at a case in which the two distributions (samples) are supposed to only differ with respect to the size.
set.seed(24)
ctrl<-rnorm(300,0,1)
dd2<-rnorm(300,0,2)
set.seed(32)
wasserstein.test(ctrl,dd2)[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 2.931697e-12 1.148397e+00 1.200000e-01 9.618000e+01 3.700000e+00
wasserstein.test(ctrl,dd2,method="ASY")[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.000005 1.148397 0.120000 96.180000 3.700000Similarly, we consider an example in which the two distributions (samples) are supposed to only differ with respect to the shape.
set.seed(24)
ctrl<-rnorm(300,6.5,sqrt(13.25))
sam1<-rnorm(300,3,1)
sam2<-rnorm(300,10,1)
dd3<-sapply(1:300,
function(n) {
sample(c(sam1[n],sam2[n]),1,prob=c(0.5, 0.5))})
set.seed(32)
wasserstein.test(ctrl,dd3)[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 2.633310e-06 2.573153e+00 1.164000e+01 0.000000e+00 8.836000e+01
wasserstein.test(ctrl,dd3,method="ASY")[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.000006 2.573153 11.640000 0.000000 88.360000Finally, we show an example in which the two distributions (samples) are supposed to be equal. We obtain a high p-value, indicating that the null hypothesis cannot be rejected.
set.seed(24)
ctrl<-rnorm(300,0,1)
nodd<-rnorm(300,0,1)
set.seed(32)
wasserstein.test(ctrl,nodd)[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.48560000 0.02772574 17.06000000 3.01000000 79.93000000
wasserstein.test(ctrl,nodd,method="ASY")[spec.output]
#> pval d.wass^2 perc.loc perc.size perc.shape
#> 0.73892700 0.02772574 17.06000000 3.01000000 79.93000000The waddR package
Detection of differential gene expression distributions in scRNAseq data
sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] BiocFileCache_2.15.0 dbplyr_2.5.0
#> [3] SingleCellExperiment_1.29.1 SummarizedExperiment_1.37.0
#> [5] Biobase_2.67.0 GenomicRanges_1.59.1
#> [7] GenomeInfoDb_1.43.2 IRanges_2.41.2
#> [9] S4Vectors_0.45.2 BiocGenerics_0.53.3
#> [11] generics_0.1.3 MatrixGenerics_1.19.0
#> [13] matrixStats_1.4.1 waddR_1.21.0
#> [15] rmarkdown_2.29
#>
#> loaded via a namespace (and not attached):
#> [1] xfun_0.49 bslib_0.8.0 lattice_0.22-6
#> [4] vctrs_0.6.5 tools_4.4.2 curl_6.0.1
#> [7] parallel_4.4.2 tibble_3.2.1 RSQLite_2.3.9
#> [10] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.7-1
#> [13] arm_1.14-4 lifecycle_1.0.4 GenomeInfoDbData_1.2.13
#> [16] compiler_4.4.2 codetools_0.2-20 eva_0.2.6
#> [19] htmltools_0.5.8.1 sys_3.4.3 buildtools_1.0.0
#> [22] sass_0.4.9 yaml_2.3.10 nloptr_2.1.1
#> [25] pillar_1.10.0 crayon_1.5.3 jquerylib_0.1.4
#> [28] MASS_7.3-61 BiocParallel_1.41.0 DelayedArray_0.33.3
#> [31] cachem_1.1.0 boot_1.3-31 abind_1.4-8
#> [34] nlme_3.1-166 tidyselect_1.2.1 digest_0.6.37
#> [37] purrr_1.0.2 dplyr_1.1.4 splines_4.4.2
#> [40] maketools_1.3.1 fastmap_1.2.0 grid_4.4.2
#> [43] SparseArray_1.7.2 cli_3.6.3 magrittr_2.0.3
#> [46] S4Arrays_1.7.1 withr_3.0.2 filelock_1.0.3
#> [49] UCSC.utils_1.3.0 bit64_4.5.2 XVector_0.47.0
#> [52] httr_1.4.7 lme4_1.1-35.5 bit_4.5.0.1
#> [55] coda_0.19-4.1 memoise_2.0.1 evaluate_1.0.1
#> [58] knitr_1.49 rlang_1.1.4 Rcpp_1.0.13-1
#> [61] glue_1.8.0 DBI_1.2.3 minqa_1.2.8
#> [64] jsonlite_1.8.9 R6_2.5.1 zlibbioc_1.52.0