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 4.2.0 RC (2022-04-21 r82226)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scTGIF_1.11.0                          
##  [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_1.39.0                     
##  [7] GenomicFeatures_1.49.0                 
##  [8] AnnotationDbi_1.59.0                   
##  [9] SingleCellExperiment_1.19.0            
## [10] SummarizedExperiment_1.27.0            
## [11] Biobase_2.57.0                         
## [12] GenomicRanges_1.49.0                   
## [13] GenomeInfoDb_1.33.1                    
## [14] IRanges_2.31.0                         
## [15] S4Vectors_0.35.0                       
## [16] MatrixGenerics_1.9.0                   
## [17] matrixStats_0.62.0                     
## [18] scTensor_2.7.0                         
## [19] RSQLite_2.2.12                         
## [20] LRBaseDbi_2.7.0                        
## [21] AnnotationHub_3.5.0                    
## [22] BiocFileCache_2.5.0                    
## [23] dbplyr_2.1.1                           
## [24] BiocGenerics_0.43.0                    
## [25] BiocStyle_2.25.0                       
## 
## loaded via a namespace (and not attached):
##   [1] ica_1.0-2                     Rsamtools_2.13.0             
##   [3] foreach_1.5.2                 lmtest_0.9-40                
##   [5] crayon_1.5.1                  spatstat.core_2.4-2          
##   [7] MASS_7.3-57                   nlme_3.1-157                 
##   [9] backports_1.4.1               GOSemSim_2.23.0              
##  [11] MeSHDbi_1.33.0                rlang_1.0.2                  
##  [13] XVector_0.37.0                ROCR_1.0-11                  
##  [15] irlba_2.3.5                   nnTensor_1.1.5               
##  [17] filelock_1.0.2                GOstats_2.63.0               
##  [19] BiocParallel_1.31.0           rjson_0.2.21                 
##  [21] tagcloud_0.6                  bit64_4.0.5                  
##  [23] glue_1.6.2                    sctransform_0.3.3            
##  [25] parallel_4.2.0                spatstat.sparse_2.1-1        
##  [27] dotCall64_1.0-1               tcltk_4.2.0                  
##  [29] DOSE_3.23.0                   spatstat.geom_2.4-0          
##  [31] tidyselect_1.1.2              SeuratObject_4.0.4           
##  [33] fitdistrplus_1.1-8            XML_3.99-0.9                 
##  [35] tidyr_1.2.0                   zoo_1.8-10                   
##  [37] GenomicAlignments_1.33.0      xtable_1.8-4                 
##  [39] magrittr_2.0.3                evaluate_0.15                
##  [41] ggplot2_3.3.5                 cli_3.3.0                    
##  [43] zlibbioc_1.43.0               miniUI_0.1.1.1               
##  [45] bslib_0.3.1                   rpart_4.1.16                 
##  [47] fastmatch_1.1-3               treeio_1.21.0                
##  [49] maps_3.4.0                    fields_13.3                  
##  [51] shiny_1.7.1                   xfun_0.30                    
##  [53] cluster_2.1.3                 tidygraph_1.2.1              
##  [55] TSP_1.2-0                     KEGGREST_1.37.0              
##  [57] tibble_3.1.6                  interactiveDisplayBase_1.35.0
##  [59] ggrepel_0.9.1                 ape_5.6-2                    
##  [61] listenv_0.8.0                 dendextend_1.15.2            
##  [63] Biostrings_2.65.0             png_0.1-7                    
##  [65] future_1.25.0                 withr_2.5.0                  
##  [67] bitops_1.0-7                  ggforce_0.3.3                
##  [69] RBGL_1.73.0                   plyr_1.8.7                   
##  [71] GSEABase_1.59.0               pillar_1.7.0                 
##  [73] cachem_1.0.6                  graphite_1.43.0              
##  [75] vctrs_0.4.1                   ellipsis_0.3.2               
##  [77] generics_0.1.2                plot3D_1.4                   
##  [79] outliers_0.15                 tools_4.2.0                  
##  [81] entropy_1.3.1                 munsell_0.5.0                
##  [83] tweenr_1.0.2                  fgsea_1.23.0                 
##  [85] DelayedArray_0.23.0           fastmap_1.1.0                
##  [87] compiler_4.2.0                abind_1.4-5                  
##  [89] httpuv_1.6.5                  rtracklayer_1.57.0           
##  [91] plotly_4.10.0                 GenomeInfoDbData_1.2.8       
##  [93] gridExtra_2.3                 lattice_0.20-45              
##  [95] deldir_1.0-6                  visNetwork_2.1.0             
##  [97] AnnotationForge_1.39.0        utf8_1.2.2                   
##  [99] later_1.3.0                   dplyr_1.0.9                  
## [101] jsonlite_1.8.0                ccTensor_1.0.2               
## [103] concaveman_1.1.0              scales_1.2.0                 
## [105] graph_1.75.0                  tidytree_0.3.9               
## [107] pbapply_1.5-0                 genefilter_1.79.0            
## [109] lazyeval_0.2.2                promises_1.2.0.1             
## [111] goftest_1.2-3                 spatstat.utils_2.3-0         
## [113] reticulate_1.24               checkmate_2.1.0              
## [115] rmarkdown_2.14                cowplot_1.1.1                
## [117] schex_1.11.0                  webshot_0.5.3                
## [119] Rtsne_0.16                    uwot_0.1.11                  
## [121] igraph_1.3.1                  survival_3.3-1               
## [123] yaml_2.3.5                    plotrix_3.8-2                
## [125] htmltools_0.5.2               memoise_2.0.1                
## [127] rTensor_1.4.8                 BiocIO_1.7.0                 
## [129] Seurat_4.1.0                  seriation_1.3.5              
## [131] graphlayouts_0.8.0            viridisLite_0.4.0            
## [133] digest_0.6.29                 assertthat_0.2.1             
## [135] ReactomePA_1.41.0             mime_0.12                    
## [137] rappdirs_0.3.3                registry_0.5-1               
## [139] spam_2.8-0                    yulab.utils_0.0.4            
## [141] future.apply_1.9.0            misc3d_0.9-1                 
## [143] data.table_1.14.2             blob_1.2.3                   
## [145] splines_4.2.0                 RCurl_1.98-1.6               
## [147] hms_1.1.1                     colorspace_2.0-3             
## [149] BiocManager_1.30.17           aplot_0.1.3                  
## [151] sass_0.4.1                    Rcpp_1.0.8.3                 
## [153] bookdown_0.26                 RANN_2.6.1                   
## [155] enrichplot_1.17.0             fansi_1.0.3                  
## [157] parallelly_1.31.1             R6_2.5.1                     
## [159] grid_4.2.0                    ggridges_0.5.3               
## [161] lifecycle_1.0.1               curl_4.3.2                   
## [163] leiden_0.3.10                 meshr_2.3.0                  
## [165] jquerylib_0.1.4               DO.db_2.9                    
## [167] Matrix_1.4-1                  qvalue_2.29.0                
## [169] RcppAnnoy_0.0.19              RColorBrewer_1.1-3           
## [171] iterators_1.0.14              stringr_1.4.0                
## [173] htmlwidgets_1.5.4             polyclip_1.10-0              
## [175] biomaRt_2.53.0                purrr_0.3.4                  
## [177] shadowtext_0.1.2              gridGraphics_0.5-1           
## [179] reactome.db_1.79.0            mgcv_1.8-40                  
## [181] globals_0.14.0                patchwork_1.1.1              
## [183] spatstat.random_2.2-0         codetools_0.2-18             
## [185] prettyunits_1.1.1             gtable_0.3.0                 
## [187] DBI_1.1.2                     ggfun_0.0.6                  
## [189] tensor_1.5                    httr_1.4.2                   
## [191] highr_0.9                     KernSmooth_2.23-20           
## [193] stringi_1.7.6                 progress_1.2.2               
## [195] msigdbr_7.5.1                 reshape2_1.4.4               
## [197] farver_2.1.0                  heatmaply_1.3.0              
## [199] annotate_1.75.0               viridis_0.6.2                
## [201] hexbin_1.28.2                 fdrtool_1.2.17               
## [203] Rgraphviz_2.41.0              magick_2.7.3                 
## [205] ggtree_3.5.0                  xml2_1.3.3                   
## [207] restfulr_0.0.13               ggplotify_0.1.0              
## [209] Category_2.63.0               scattermore_0.8              
## [211] BiocVersion_3.16.0            bit_4.0.4                    
## [213] scatterpie_0.1.7              spatstat.data_2.2-0          
## [215] ggraph_2.0.5                  babelgene_22.3               
## [217] pkgconfig_2.0.3               knitr_1.39