unused arguments (min.dist = 0.3, n.neighbors = k)
yueli8 opened this issue · 1 comments
yueli8 commented
Hello,
Thank you for developing so nice software!
Thank you in advance for great help!
Best,
Yue
> cellchat <- netEmbedding(cellchat, type = "functional")
Manifold learning of the signaling networks for datasets 1 2
Error in runUMAP(Similarity, min.dist = 0.3, n.neighbors = k) :
unused arguments (min.dist = 0.3, n.neighbors = k)
> library(umap-learn)
Error in library(umap - learn) : 'package' must be of length 1
> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=zh_CN.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] umap_0.2.10.0 glmGamPoi_1.12.2 reticulate_1.34.0 uwot_0.1.16 Matrix_1.6-5 patchwork_1.2.0 anndata_0.7.5.6 ggalluvial_0.12.5
[9] Seurat_5.0.1 SeuratObject_5.0.1 sp_2.1-2 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[17] tidyr_1.3.0 tibble_3.2.1 tidyverse_2.0.0 CellChat_1.6.1 ggplot2_3.4.4 igraph_1.3.5 dplyr_1.1.4 bigmemory_4.6.4
[25] Biobase_2.60.0 BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.21 splines_4.3.0 later_1.3.2 bitops_1.0-7 polyclip_1.10-6
[6] ggnetwork_0.5.12 fastDummies_1.7.3 lifecycle_1.0.4 rstatix_0.7.2 rprojroot_2.0.4
[11] doParallel_1.0.17 globals_0.16.2 lattice_0.22-5 MASS_7.3-60 backports_1.4.1
[16] magrittr_2.0.3 plotly_4.10.4 httpuv_1.6.13 NMF_0.26 sctransform_0.4.1
[21] askpass_1.2.0 spam_2.10-0 spatstat.sparse_3.0-3 cowplot_1.1.2 pbapply_1.7-2
[26] RColorBrewer_1.1-3 zlibbioc_1.46.0 abind_1.4-5 GenomicRanges_1.52.1 Rtsne_0.17
[31] RCurl_1.98-1.14 rappdirs_0.3.3 GenomeInfoDbData_1.2.10 circlize_0.4.15 IRanges_2.34.1
[36] S4Vectors_0.38.2 ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.0 spatstat.utils_3.0-4
[41] goftest_1.2-3 RSpectra_0.16-1 spatstat.random_3.2-2 fitdistrplus_1.1-11 parallelly_1.36.0
[46] svglite_2.1.3 DelayedArray_0.26.7 leiden_0.4.3.1 codetools_0.2-19 tidyselect_1.2.0
[51] shape_1.4.6 farver_2.1.1 matrixStats_1.2.0 stats4_4.3.0 spatstat.explore_3.2-5
[56] jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.18.0 ellipsis_0.3.2 progressr_0.14.0
[61] ggridges_0.5.5 survival_3.5-7 iterators_1.0.14 systemfonts_1.0.5 foreach_1.5.2
[66] tools_4.3.0 ragg_1.2.7 sna_2.7-2 ica_1.0-3 Rcpp_1.0.12
[71] glue_1.7.0 gridExtra_2.3 here_1.0.1 MatrixGenerics_1.12.3 GenomeInfoDb_1.36.4
[76] withr_2.5.2 BiocManager_1.30.22 fastmap_1.1.1 fansi_1.0.5 openssl_2.1.1
[81] digest_0.6.34 timechange_0.2.0 R6_2.5.1 mime_0.12 textshaping_0.3.7
[86] colorspace_2.1-0 Cairo_1.6-2 scattermore_1.2 tensor_1.5 spatstat.data_3.0-3
[91] utf8_1.2.4 generics_0.1.3 data.table_1.14.10 FNN_1.1.3.2 S4Arrays_1.0.6
[96] httr_1.4.7 htmlwidgets_1.6.4 pkgconfig_2.0.3 gtable_0.3.4 registry_0.5-1
[101] ComplexHeatmap_2.16.0 lmtest_0.9-40 XVector_0.40.0 htmltools_0.5.7 carData_3.0-5
[106] dotCall64_1.1-1 clue_0.3-65 scales_1.3.0 png_0.1-8 bigmemory.sri_0.1.8
[111] rstudioapi_0.15.0 tzdb_0.4.0 reshape2_1.4.4 rjson_0.2.21 uuid_1.1-1
[116] coda_0.19-4 statnet.common_4.9.0 nlme_3.1-164 zoo_1.8-12 GlobalOptions_0.1.2
[121] KernSmooth_2.23-22 vipor_0.4.7 parallel_4.3.0 miniUI_0.1.1.1 ggrastr_1.0.2
[126] pillar_1.9.0 grid_4.3.0 vctrs_0.6.5 RANN_2.6.1 promises_1.2.1
[131] ggpubr_0.6.0 car_3.1-2 xtable_1.8-4 cluster_2.1.6 beeswarm_0.4.0
[136] magick_2.8.2 cli_3.6.2 compiler_4.3.0 rlang_1.1.3 crayon_1.5.2
[141] rngtools_1.5.2 future.apply_1.11.1 ggsignif_0.6.4 labeling_0.4.3 ggbeeswarm_0.7.2
[146] plyr_1.8.9 stringi_1.8.3 viridisLite_0.4.2 network_1.18.2 deldir_2.0-2
[151] gridBase_0.4-7 BiocParallel_1.34.2 assertthat_0.2.1 munsell_0.5.0 lazyeval_0.2.2
[156] spatstat.geom_3.2-7 RcppHNSW_0.5.0 hms_1.1.3 future_1.33.1 shiny_1.8.0
[161] SummarizedExperiment_1.30.2 ROCR_1.0-11 broom_1.0.5
yueli8 commented
library(NMF)