hdWGCNA
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Published
20 hours ago •
smorabit
smorabit
maybe wrong hub genes orders in PlotKMEs
question
Hi @smorabit ,thanks for your convenient tool! After PlotKMEs, I wonder whether the gene symbols on the right side are in the opposite order compared with the original hub_df? In my opinion, the gene with the largest kME value will be arranged in the first row from top to bottom.
session
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 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-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] splines stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggradar_0.2 hdWGCNA_0.3.03 UCell_2.8.0
[4] igraph_2.0.3 ggrepel_0.9.6 harmony_1.2.1
[7] Rcpp_1.0.13 WGCNA_1.73 fastcluster_1.2.6
[10] dynamicTreeCut_1.63-1 patchwork_1.2.0 cowplot_1.1.3
[13] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[16] purrr_1.0.2 readr_2.1.5 tibble_3.2.1
[19] tidyverse_2.0.0 infercnv_1.20.0 survminer_0.4.9
[22] ggpubr_0.6.0 survival_3.7-0 sesameData_1.22.0
[25] ExperimentHub_2.12.0 AnnotationHub_3.12.0 BiocFileCache_2.12.0
[28] dbplyr_2.3.4 SummarizedExperiment_1.34.0 GenomicRanges_1.56.1
[31] GenomeInfoDb_1.40.1 IRanges_2.38.0 S4Vectors_0.42.0
[34] MatrixGenerics_1.16.0 matrixStats_1.3.0 TCGAbiolinks_2.32.0
[37] scales_1.3.0 lsa_0.73.3 SnowballC_0.7.1
[40] pheatmap_1.0.12 ggalluvial_0.12.5 tidyr_1.3.1
[43] distdimscr_0.0.0.9000 knitr_1.47 Seurat_5.1.0
[46] SeuratObject_5.0.2 monocle_2.32.0 DDRTree_0.1.5
[49] irlba_2.3.5.1 VGAM_1.1-11 Biobase_2.64.0
[52] BiocGenerics_0.48.1 Matrix_1.7-0 dittoSeq_1.16.0
[55] dplyr_1.1.4 ggplot2_3.5.1 sp_2.1-4
loaded via a namespace (and not attached):
[1] ica_1.0-3 plotly_4.10.4 Formula_1.2-5
[4] devtools_2.4.5 zlibbioc_1.50.0 tidyselect_1.2.1
[7] rvest_1.0.4 bit_4.0.5 doParallel_1.0.17
[10] lattice_0.22-6 urlchecker_1.0.1 blob_1.2.4
[13] S4Arrays_1.4.1 parallel_4.4.1 png_0.1-8
[16] cli_3.6.2 ggplotify_0.1.2 goftest_1.2-3
[19] textshaping_0.4.0 BiocNeighbors_1.22.0 uwot_0.2.2
[22] shadowtext_0.1.3 curl_5.2.1 mime_0.12
[25] evaluate_0.24.0 tidytree_0.4.6 leiden_0.4.3.1
[28] coin_1.4-3 stringi_1.8.4 desc_1.4.3
[31] backports_1.5.0 rjags_4-16 parallelDist_0.2.6
[34] XML_3.99-0.16.1 httpuv_1.6.15 AnnotationDbi_1.66.0
[37] magrittr_2.0.3 clusterProfiler_4.12.0 rappdirs_0.3.3
[40] KMsurv_0.1-5 ggraph_2.2.1 sctransform_0.4.1
[43] sessioninfo_1.2.2 DBI_1.2.3 withr_3.0.0
[46] systemfonts_1.1.0 enrichplot_1.24.0 lmtest_0.9-40
[49] tidygraph_1.3.1 formatR_1.14 BiocManager_1.30.23
[52] htmlwidgets_1.6.4 fs_1.6.4 biomaRt_2.60.1
[55] SingleCellExperiment_1.22.0 labeling_0.4.3 SparseArray_1.4.8
[58] reticulate_1.38.0 zoo_1.8-12 XVector_0.44.0
[61] UCSC.utils_1.0.0 RhpcBLASctl_0.23-42 timechange_0.3.0
[64] foreach_1.5.2 fansi_1.0.6 caTools_1.18.2
[67] grid_4.4.1 data.table_1.15.4 ggtree_3.12.0
[70] R.oo_1.26.0 RSpectra_0.16-1 tester_0.2.0
[73] fastDummies_1.7.3 gridGraphics_0.5-1 ellipsis_0.3.2
[76] lazyeval_0.2.2 yaml_2.3.8 phyclust_0.1-34
[79] scattermore_1.2 BiocVersion_3.19.1 crayon_1.5.3
[82] TCGAbiolinksGUI.data_1.24.0 RcppAnnoy_0.0.22 RColorBrewer_1.1-3
[85] progressr_0.14.0 tweenr_2.0.3 later_1.3.2
[88] profvis_0.3.8 ggridges_0.5.6 codetools_0.2-20
[91] base64enc_0.1-3 HSMMSingleCell_1.24.0 KEGGREST_1.44.1
[94] Rtsne_0.17 fastICA_1.2-4 limma_3.60.3
[97] filelock_1.0.3 foreign_0.8-86 pkgconfig_2.0.3
[100] xml2_1.3.6 aplot_0.2.3 spatstat.sparse_3.1-0
[103] ape_5.8 viridisLite_0.4.2 xtable_1.8-4
[106] car_3.1-2 plyr_1.8.9 httr_1.4.7
[109] tools_4.4.1 globals_0.16.3 pkgbuild_1.4.4
[112] htmlTable_2.4.3 broom_1.0.6 checkmate_2.3.1
[115] nlme_3.1-165 futile.logger_1.4.3 lambda.r_1.2.4
[118] HDO.db_0.99.1 hdf5r_1.3.10 survMisc_0.5.6
[121] digest_0.6.36 farver_2.1.2 tzdb_0.4.0
[124] reshape2_1.4.4 yulab.utils_0.1.4 viridis_0.6.5
[127] rpart_4.1.23 glue_1.7.0 cachem_1.1.0
[130] polyclip_1.10-6 Hmisc_5.1-3 generics_0.1.3
[133] Biostrings_2.72.1 mvtnorm_1.2-5 parallelly_1.37.1
[136] pkgload_1.3.4 statmod_1.5.0 impute_1.78.0
[139] RcppHNSW_0.6.0 ragg_1.3.2 carData_3.0-5
[142] pbapply_1.7-2 httr2_1.0.1 spam_2.10-0
[145] gson_0.1.0 utf8_1.2.4 graphlayouts_1.1.1
[148] gtools_3.9.5 preprocessCore_1.66.0 ggsignif_0.6.4
[151] gridExtra_2.3 shiny_1.8.1.1 GenomeInfoDbData_1.2.12
[154] R.utils_2.12.3 RCurl_1.98-1.14 memoise_2.0.1
[157] rmarkdown_2.27 downloader_0.4 R.methodsS3_1.8.2
[160] future_1.33.2 RANN_2.6.1 km.ci_0.5-6
[163] spatstat.data_3.1-2 rstudioapi_0.16.0 cluster_2.1.6
[166] spatstat.utils_3.0-5 hms_1.1.3 fitdistrplus_1.1-11
[169] munsell_0.5.1 colorspace_2.1-0 FNN_1.1.4
[172] rlang_1.1.3 dotCall64_1.1-1 ggforce_0.4.2
[175] xfun_0.45 coda_0.19-4.1 TH.data_1.1-2
[178] remotes_2.5.0 iterators_1.0.14 modeltools_0.2-23
[181] abind_1.4-5 GOSemSim_2.30.0 libcoin_1.0-10
[184] treeio_1.28.0 ps_1.7.6 futile.options_1.0.1
[187] bitops_1.0-7 promises_1.3.0 scatterpie_0.2.3
[190] RSQLite_2.3.7 leidenbase_0.1.27 qvalue_2.36.0
[193] sandwich_3.1-1 fgsea_1.30.0 DelayedArray_0.30.1
[196] proxy_0.4-27 GO.db_3.19.1 compiler_4.4.1
[199] prettyunits_1.2.0 listenv_0.9.1 edgeR_4.2.0
[202] tensor_1.5 usethis_2.2.3 MASS_7.3-61
[205] progress_1.2.3 BiocParallel_1.38.0 spatstat.random_3.2-3
[208] R6_2.5.1 fastmap_1.2.0 multcomp_1.4-26
[211] fastmatch_1.1-4 rstatix_0.7.2 ROCR_1.0-11
[214] nnet_7.3-19 gtable_0.3.5 KernSmooth_2.23-24
[217] miniUI_0.1.1.1 deldir_2.0-4 gitcreds_0.1.2
[220] htmltools_0.5.8.1 RcppParallel_5.1.9 bit64_4.0.5
[223] spatstat.explore_3.2-7 lifecycle_1.0.4 processx_3.8.4
[226] callr_3.7.6 vctrs_0.6.5 MuDataSeurat_0.0.1.0000
[229] slam_0.1-50 spatstat.geom_3.2-9 DOSE_3.30.1
[232] ggfun_0.1.5 future.apply_1.11.2 pillar_1.9.0
[235] gplots_3.1.3.1 locfit_1.5-9.9 combinat_0.0-8
[238] jsonlite_1.8.8 argparse_2.2.3
