Contents

1 Summary of the output objects of scTensor

Here, we introduced the objects saved in reanalysis.RData.

library("scTensor")
load("reanalysis.RData")

After performing cellCellReport, some R objects are saved in the reanalysis.RData as follows;

2 Execution of scTensor with the different options

Using the reanalysis.RData, some users may want to perform scTensor with different parameters.

For example, some users want to perform cellCellDecomp with different ranks, perform cellCellReport with omitting some enrichment analysis, provide the results to their collaborators.

To do such tasks, just type like belows.

library("AnnotationHub")
library("LRBaseDbi")

# Create LRBase object
ah <- AnnotationHub()
dbfile <- query(ah, c("LRBaseDb", "Homo sapiens", "v002"))[[1]]
LRBase.Hsa.eg.db <- LRBaseDbi::LRBaseDb(dbfile)

# Register the file pass of user's LRBase
metadata(sce)$lrbase <- dbfile(LRBase.Hsa.eg.db)

# CCI Tensor Decomposition
cellCellDecomp(sce, ranks=c(6,5), assayNames="normcounts")

# HTML Report
cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts",
    title="Cell-cell interaction within Germline_Male, GSE86146",
    author="Koki Tsuyuzaki", html.open=TRUE,
    goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE,
    doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE)

Session information

## R version 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scTGIF_1.12.0                          
##  [2] Homo.sapiens_1.3.1                     
##  [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [4] org.Hs.eg.db_3.15.0                    
##  [5] GO.db_3.15.0                           
##  [6] OrganismDbi_1.40.0                     
##  [7] GenomicFeatures_1.50.2                 
##  [8] AnnotationDbi_1.60.0                   
##  [9] SingleCellExperiment_1.20.0            
## [10] SummarizedExperiment_1.28.0            
## [11] Biobase_2.58.0                         
## [12] GenomicRanges_1.50.1                   
## [13] GenomeInfoDb_1.34.2                    
## [14] IRanges_2.32.0                         
## [15] S4Vectors_0.36.0                       
## [16] MatrixGenerics_1.10.0                  
## [17] matrixStats_0.62.0                     
## [18] scTensor_2.8.0                         
## [19] RSQLite_2.2.14                         
## [20] LRBaseDbi_2.8.0                        
## [21] AnnotationHub_3.6.0                    
## [22] BiocFileCache_2.6.0                    
## [23] dbplyr_2.2.1                           
## [24] BiocGenerics_0.44.0                    
## [25] BiocStyle_2.26.0                       
## 
## loaded via a namespace (and not attached):
##   [1] ica_1.0-3                     Rsamtools_2.14.0             
##   [3] foreach_1.5.2                 lmtest_0.9-40                
##   [5] crayon_1.5.1                  spatstat.core_2.4-4          
##   [7] MASS_7.3-58                   nlme_3.1-158                 
##   [9] backports_1.4.1               GOSemSim_2.24.0              
##  [11] MeSHDbi_1.34.0                rlang_1.0.4                  
##  [13] XVector_0.38.0                HDO.db_0.99.1                
##  [15] ROCR_1.0-11                   irlba_2.3.5                  
##  [17] nnTensor_1.1.8                filelock_1.0.2               
##  [19] GOstats_2.64.0                rjson_0.2.21                 
##  [21] BiocParallel_1.32.1           tagcloud_0.6                 
##  [23] bit64_4.0.5                   glue_1.6.2                   
##  [25] sctransform_0.3.3             parallel_4.2.1               
##  [27] spatstat.sparse_2.1-1         dotCall64_1.0-1              
##  [29] tcltk_4.2.1                   DOSE_3.24.1                  
##  [31] spatstat.geom_2.4-0           tidyselect_1.1.2             
##  [33] SeuratObject_4.1.0            fitdistrplus_1.1-8           
##  [35] XML_3.99-0.10                 tidyr_1.2.0                  
##  [37] zoo_1.8-10                    GenomicAlignments_1.34.0     
##  [39] xtable_1.8-4                  magrittr_2.0.3               
##  [41] evaluate_0.15                 ggplot2_3.3.6                
##  [43] cli_3.3.0                     zlibbioc_1.44.0              
##  [45] miniUI_0.1.1.1                sp_1.5-0                     
##  [47] bslib_0.3.1                   rpart_4.1.16                 
##  [49] fastmatch_1.1-3               treeio_1.22.0                
##  [51] maps_3.4.0                    fields_14.0                  
##  [53] shiny_1.7.1                   xfun_0.31                    
##  [55] gson_0.0.6                    cluster_2.1.3                
##  [57] tidygraph_1.2.1               TSP_1.2-1                    
##  [59] KEGGREST_1.38.0               tibble_3.1.7                 
##  [61] interactiveDisplayBase_1.36.0 ggrepel_0.9.1                
##  [63] ape_5.6-2                     listenv_0.8.0                
##  [65] dendextend_1.16.0             Biostrings_2.66.0            
##  [67] png_0.1-7                     future_1.26.1                
##  [69] bitops_1.0-7                  ggforce_0.3.3                
##  [71] RBGL_1.74.0                   plyr_1.8.7                   
##  [73] GSEABase_1.60.0               pillar_1.7.0                 
##  [75] cachem_1.0.6                  graphite_1.44.0              
##  [77] vctrs_0.4.1                   ellipsis_0.3.2               
##  [79] generics_0.1.3                plot3D_1.4                   
##  [81] rgdal_1.5-32                  outliers_0.15                
##  [83] tools_4.2.1                   entropy_1.3.1                
##  [85] munsell_0.5.0                 tweenr_1.0.2                 
##  [87] fgsea_1.24.0                  DelayedArray_0.24.0          
##  [89] fastmap_1.1.0                 compiler_4.2.1               
##  [91] abind_1.4-5                   httpuv_1.6.5                 
##  [93] rtracklayer_1.58.0            plotly_4.10.0                
##  [95] rgeos_0.5-9                   GenomeInfoDbData_1.2.8       
##  [97] gridExtra_2.3                 lattice_0.20-45              
##  [99] deldir_1.0-6                  visNetwork_2.1.0             
## [101] AnnotationForge_1.40.0        utf8_1.2.2                   
## [103] later_1.3.0                   dplyr_1.0.9                  
## [105] jsonlite_1.8.0                ccTensor_1.0.2               
## [107] concaveman_1.1.0              scales_1.2.0                 
## [109] graph_1.76.0                  tidytree_0.3.9               
## [111] pbapply_1.5-0                 genefilter_1.80.0            
## [113] lazyeval_0.2.2                promises_1.2.0.1             
## [115] goftest_1.2-3                 spatstat.utils_2.3-1         
## [117] reticulate_1.25               checkmate_2.1.0              
## [119] rmarkdown_2.14                cowplot_1.1.1                
## [121] schex_1.12.0                  webshot_0.5.3                
## [123] Rtsne_0.16                    uwot_0.1.11                  
## [125] igraph_1.3.5                  survival_3.3-1               
## [127] yaml_2.3.5                    plotrix_3.8-2                
## [129] htmltools_0.5.2               memoise_2.0.1                
## [131] rTensor_1.4.8                 BiocIO_1.8.0                 
## [133] Seurat_4.1.1                  seriation_1.3.5              
## [135] graphlayouts_0.8.0            viridisLite_0.4.0            
## [137] digest_0.6.29                 assertthat_0.2.1             
## [139] ReactomePA_1.42.0             mime_0.12                    
## [141] rappdirs_0.3.3                registry_0.5-1               
## [143] spam_2.9-0                    yulab.utils_0.0.5            
## [145] future.apply_1.9.0            misc3d_0.9-1                 
## [147] data.table_1.14.2             blob_1.2.3                   
## [149] splines_4.2.1                 RCurl_1.98-1.7               
## [151] hms_1.1.1                     colorspace_2.0-3             
## [153] BiocManager_1.30.18           aplot_0.1.6                  
## [155] sass_0.4.1                    Rcpp_1.0.9                   
## [157] bookdown_0.27                 RANN_2.6.1                   
## [159] enrichplot_1.18.0             fansi_1.0.3                  
## [161] parallelly_1.32.0             R6_2.5.1                     
## [163] grid_4.2.1                    ggridges_0.5.3               
## [165] lifecycle_1.0.1               curl_4.3.2                   
## [167] leiden_0.4.2                  meshr_2.4.0                  
## [169] jquerylib_0.1.4               Matrix_1.4-1                 
## [171] qvalue_2.30.0                 RcppAnnoy_0.0.19             
## [173] RColorBrewer_1.1-3            iterators_1.0.14             
## [175] stringr_1.4.0                 htmlwidgets_1.5.4            
## [177] polyclip_1.10-0               biomaRt_2.54.0               
## [179] purrr_0.3.4                   shadowtext_0.1.2             
## [181] gridGraphics_0.5-1            reactome.db_1.81.0           
## [183] mgcv_1.8-40                   globals_0.15.1               
## [185] patchwork_1.1.1               spatstat.random_2.2-0        
## [187] progressr_0.10.1              codetools_0.2-18             
## [189] prettyunits_1.1.1             gtable_0.3.0                 
## [191] DBI_1.1.3                     ggfun_0.0.6                  
## [193] tensor_1.5                    httr_1.4.3                   
## [195] highr_0.9                     KernSmooth_2.23-20           
## [197] stringi_1.7.8                 progress_1.2.2               
## [199] msigdbr_7.5.1                 reshape2_1.4.4               
## [201] farver_2.1.1                  heatmaply_1.3.0              
## [203] annotate_1.76.0               viridis_0.6.2                
## [205] hexbin_1.28.2                 fdrtool_1.2.17               
## [207] Rgraphviz_2.42.0              magick_2.7.3                 
## [209] ggtree_3.6.0                  xml2_1.3.3                   
## [211] restfulr_0.0.15               ggplotify_0.1.0              
## [213] Category_2.64.0               scattermore_0.8              
## [215] BiocVersion_3.16.0            bit_4.0.4                    
## [217] scatterpie_0.1.7              spatstat.data_2.2-0          
## [219] ggraph_2.0.5                  babelgene_22.3               
## [221] pkgconfig_2.0.3               knitr_1.39