library(MAAS)
library(tidydr)
library(withr)
# Set seed for reproducibility
set.seed(1234)
# Load example data
data("maas_example")
# Run MAAS
maas.test <- MAAS(maas_example$Peak, maas_example$CNV, maas_example$SNV, dims = 2:5)
## Training when k=2
## Training when k=3
## Training when k=4
## Training when k=5
# Evaluate clustering performance
clusPerformance <- data.frame(matrix(nrow = length(maas.test)-1, ncol = 5),
row.names = paste0("dims=", 2:length(maas.test)))
colnames(clusPerformance) <- paste0("k=", 2:6)
for(i in 1:(length(maas.test)-1)){
for(j in 2:6){
df <- as.data.frame(maas.test[[i]]$W)
maas.tmp.clu <- with_seed(2, kmeans(df, centers = j)$cluster)
clusPerformance[i,j-1] <- clusteringMetric(maas.test[[i]]$W, clu = maas.tmp.clu, disMethod = "cosine")
}
}
clusPerformance
## k=2 k=3 k=4 k=5 k=6
## dims=2 7.6580070 0.04792606 0.001519815 0.0003074383 0.000000e+00
## dims=3 0.1610961 0.10854696 0.011809798 0.0666966181 3.026747e-03
## dims=4 0.1280585 0.05573401 0.015179780 0.0071901979 1.336539e-05
## dims=5 0.2274295 0.09587623 0.006809193 0.0052164072 1.387891e-02
# Select one layer and perform clustering
df <- as.data.frame(maas.test[[1]]$W)
maas.clu <- data.frame(Cluster = with_seed(2, kmeans(df, centers = 2)$cluster))
maas.clu$Cluster <- as.factor(maas.clu$Cluster)
# Compute UMAP
umap.axis <- with_seed(2, umap(df, n_neighbors = 10, metric = "correlation"))
umap.axis <- as.data.frame(umap.axis)
umap.axis$Cluster <- maas.clu$Cluster
colnames(umap.axis) <- c("UMAP-1", "UMAP-2", "Cluster")
# UMAP plot
ggplot(umap.axis, aes(`UMAP-1`, `UMAP-2`)) +
geom_point(aes(color = Cluster), size = 1.75) +
theme_dr()+
labs(x = "UMAP-1", y = "UMAP-2")+
theme(panel.grid = element_blank(),
axis.title = element_text(size = 14),
axis.text = element_blank(),
legend.text = element_text(size = 12))
sessionInfo()
## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
## [5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
## [7] LC_PAPER=en_HK.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Asia/Hong_Kong
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] MAAS_1.0.0 tidydr_0.0.5 uwot_0.1.16 Matrix_1.6-3
## [5] ggplot2_3.4.4 withr_3.0.2 clValid_0.7 fpc_2.2-12
## [9] parallelDist_0.2.6 clusterSim_0.51-3 MASS_7.3-60 cluster_2.1.5
##
## loaded via a namespace (and not attached):
## [1] ade4_1.7-22 tidyselect_1.2.0 farver_2.1.1 dplyr_1.1.4
## [5] fastmap_1.1.1 promises_1.2.1 digest_0.6.33 mime_0.12
## [9] lifecycle_1.0.4 ellipsis_0.3.2 processx_3.8.2 magrittr_2.0.3
## [13] kernlab_0.9-32 compiler_4.3.2 rlang_1.1.2 sass_0.4.7
## [17] tools_4.3.2 utf8_1.2.4 yaml_2.3.7 knitr_1.45
## [21] labeling_0.4.3 prettyunits_1.2.0 htmlwidgets_1.6.3 pkgbuild_1.4.2
## [25] mclust_6.1.1 pkgload_1.3.3 R2HTML_2.3.4 miniUI_0.1.1.1
## [29] purrr_1.0.2 nnet_7.3-19 grid_4.3.2 stats4_4.3.2
## [33] fansi_1.0.5 urlchecker_1.0.1 profvis_0.3.8 xtable_1.8-4
## [37] e1071_1.7-13 colorspace_2.1-0 scales_1.3.0 prabclus_2.3-3
## [41] cli_3.6.1 rmarkdown_2.25 crayon_1.5.2 generics_0.1.3
## [45] remotes_2.4.2.1 RcppParallel_5.1.7 rstudioapi_0.15.0 robustbase_0.99-2
## [49] sessioninfo_1.2.2 cachem_1.0.8 proxy_0.4-27 stringr_1.5.1
## [53] modeltools_0.2-23 parallel_4.3.2 vctrs_0.6.4 devtools_2.4.5
## [57] jsonlite_1.8.7 callr_3.7.3 diptest_0.77-1 jquerylib_0.1.4
## [61] glue_1.6.2 DEoptimR_1.1-3 codetools_0.2-19 ps_1.7.5
## [65] RcppAnnoy_0.0.21 stringi_1.8.2 gtable_0.3.4 later_1.3.1
## [69] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0 htmltools_0.5.7
## [73] R6_2.5.1 evaluate_1.0.3 shiny_1.8.0 lattice_0.22-5
## [77] highr_0.10 memoise_2.0.1 httpuv_1.6.12 ggfun_0.1.3
## [81] bslib_0.6.0 class_7.3-22 Rcpp_1.0.11 flexmix_2.3-19
## [85] xfun_0.41 fs_1.6.3 usethis_2.2.2 pkgconfig_2.0.3