vertex.label.cex not changing label size in ModuleUMAPPlot output

[EbmeyerSt]

Hi, Thank you for creating a great WGCNA package! I think there is a small bug in the ModuleUMAPPlot function regarding the adjustment of hub gene label sizes in the output. Changing the vertex.label.cex value does not seem to have any effect on the label size.

This is how I run the function:

  pdf(file.path(outpath, (paste0('Network_plots/',abbrv_name,'_Network_UMAP.pdf'))), width = 6, height = 7)
    ModuleUMAPPlot(
        obj,
        edge.alpha = 0.25,
        sample_edges = TRUE,
        edge_prop = 0.15,
        label_hubs = 2,
        keep_grey_edges = FALSE,
        vertex.label.cex = 0.5,
        wgcna_name = obj@misc$active_wgcna
      )
  dev.off()

Wondering if this is a bug or I am missing something, would appreciate feedback on this!

R session info R version 4.5.0 (2025-04-11) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

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: Europe/Stockholm tzcode source: internal

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

other attached packages: [1] future_1.58.0 ggradar_0.2 maSigPro_1.80.0 ggforestplot_0.1.0 org.Dr.eg.db_3.21.0
[6] topGO_2.59.0 SparseM_1.84-2 GO.db_3.21.0 AnnotationDbi_1.70.0 Biobase_2.68.0
[11] graph_1.86.0 NetRep_1.2.7 fgsea_1.34.0 enrichR_3.4 lubridate_1.9.4
[16] forcats_1.0.0 stringr_1.5.1 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[21] tibble_3.3.0 tidyverse_2.0.0 magrittr_2.0.3 patchwork_1.3.0 hdWGCNA_0.4.06
[26] tidygraph_1.3.1 ggraph_2.2.1 igraph_2.1.4 dplyr_1.1.4 ggrepel_0.9.6
[31] ggplot2_3.5.2 harmony_1.2.3 Rcpp_1.0.14 GeneOverlap_1.44.0 GenomicRanges_1.60.0 [36] GenomeInfoDb_1.44.0 IRanges_2.42.0 S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.4
[41] WGCNA_1.73 fastcluster_1.3.0 dynamicTreeCut_1.63-1 UCell_2.12.0 BiocManager_1.30.26
[46] devtools_2.4.5 usethis_3.1.0 Seurat_5.3.0 SeuratObject_5.1.0 sp_2.2-0

loaded via a namespace (and not attached): [1] fs_1.6.6 matrixStats_1.5.0 spatstat.sparse_3.1-0 bitops_1.0-9
[5] httr_1.4.7 RColorBrewer_1.1-3 doParallel_1.0.17 profvis_0.4.0
[9] tools_4.5.0 sctransform_0.4.2 backports_1.5.0 R6_2.6.1
[13] lazyeval_0.2.2 uwot_0.2.3 urlchecker_1.0.1 withr_3.0.2
[17] gridExtra_2.3 preprocessCore_1.70.0 progressr_0.15.1 textshaping_1.0.1
[21] cli_3.6.5 spatstat.explore_3.4-3 fastDummies_1.7.5 labeling_0.4.3
[25] spatstat.data_3.1-6 proxy_0.4-27 ggridges_0.5.6 pbapply_1.7-2
[29] systemfonts_1.2.3 foreign_0.8-90 WriteXLS_6.8.0 parallelly_1.45.0
[33] sessioninfo_1.2.3 rstudioapi_0.17.1 impute_1.82.0 RSQLite_2.4.1
[37] FNN_1.1.4.1 gtools_3.9.5 ica_1.0-3 spatstat.random_3.4-1
[41] Matrix_1.7-3 abind_1.4-8 lifecycle_1.0.4 yaml_2.3.10
[45] SummarizedExperiment_1.38.1 gplots_3.2.0 SparseArray_1.8.0 Rtsne_0.17
[49] grid_4.5.0 blob_1.2.4 promises_1.3.3 venn_1.12
[53] crayon_1.5.3 miniUI_0.1.2 lattice_0.22-7 cowplot_1.1.3
[57] KEGGREST_1.48.0 pillar_1.10.2 knitr_1.50 rjson_0.2.23
[61] admisc_0.38 future.apply_1.20.0 codetools_0.2-20 fastmatch_1.1-6
[65] glue_1.8.0 spatstat.univar_3.1-3 data.table_1.17.4 remotes_2.5.0
[69] vctrs_0.6.5 png_0.1-8 spam_2.11-1 gtable_0.3.6
[73] cachem_1.1.0 xfun_0.52 S4Arrays_1.8.1 mime_0.13
[77] survival_3.8-3 SingleCellExperiment_1.30.1 iterators_1.0.14 statmod_1.5.0
[81] ellipsis_0.3.2 fitdistrplus_1.2-2 ROCR_1.0-11 nlme_3.1-168
[85] bit64_4.6.0-1 RcppAnnoy_0.0.22 irlba_2.3.5.1 KernSmooth_2.23-26
[89] rpart_4.1.24 colorspace_2.1-1 DBI_1.2.3 Hmisc_5.2-3
[93] nnet_7.3-20 tidyselect_1.2.1 curl_6.3.0 bit_4.6.0
[97] compiler_4.5.0 htmlTable_2.4.3 BiocNeighbors_2.2.0 DelayedArray_0.34.1
[101] plotly_4.10.4 checkmate_2.3.2 scales_1.4.0 caTools_1.18.3
[105] lmtest_0.9-40 digest_0.6.37 goftest_1.2-3 spatstat.utils_3.1-4
[109] rmarkdown_2.29 RhpcBLASctl_0.23-42 XVector_0.48.0 htmltools_0.5.8.1
[113] pkgconfig_2.0.3 base64enc_0.1-3 MatrixGenerics_1.20.0 fastmap_1.2.0
[117] rlang_1.1.6 htmlwidgets_1.6.4 UCSC.utils_1.4.0 shiny_1.10.0
[121] farver_2.1.2 zoo_1.8-14 jsonlite_2.0.0 mclust_6.1.1
[125] BiocParallel_1.42.1 Formula_1.2-5 GenomeInfoDbData_1.2.14 dotCall64_1.2
[129] viridis_0.6.5 reticulate_1.42.0 stringi_1.8.7 MASS_7.3-65
[133] plyr_1.8.9 pkgbuild_1.4.8 parallel_4.5.0 listenv_0.9.1
[137] deldir_2.0-4 Biostrings_2.76.0 graphlayouts_1.2.2 splines_4.5.0
[141] tensor_1.5 hms_1.1.3 spatstat.geom_3.4-1 RcppHNSW_0.6.0
[145] reshape2_1.4.4 pkgload_1.4.0 evaluate_1.0.3 tester_0.2.0
[149] tzdb_0.5.0 foreach_1.5.2 tweenr_2.0.3 httpuv_1.6.16
[153] RANN_2.6.2 polyclip_1.10-7 scattermore_1.2 ggforce_0.4.2
[157] broom_1.0.8 xtable_1.8-4 RSpectra_0.16-2 later_1.4.2
[161] ragg_1.4.0 viridisLite_0.4.2 memoise_2.0.1 cluster_2.1.8.1
[165] timechange_0.3.0 globals_0.18.0