unused arguments (min.dist = 0.3, n.neighbors = k)

[yueli8]

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]

library(NMF)