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 Under development (unstable) (2021-10-19 r81077)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-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_1.9.0                           
##  [2] Homo.sapiens_1.3.1                     
##  [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [4] org.Hs.eg.db_3.14.0                    
##  [5] GO.db_3.14.0                           
##  [6] OrganismDbi_1.37.0                     
##  [7] GenomicFeatures_1.47.1                 
##  [8] AnnotationDbi_1.57.0                   
##  [9] SingleCellExperiment_1.17.0            
## [10] SummarizedExperiment_1.25.0            
## [11] Biobase_2.55.0                         
## [12] GenomicRanges_1.47.1                   
## [13] GenomeInfoDb_1.31.0                    
## [14] IRanges_2.29.0                         
## [15] S4Vectors_0.33.0                       
## [16] MatrixGenerics_1.7.0                   
## [17] matrixStats_0.61.0                     
## [18] scTensor_2.5.0                         
## [19] RSQLite_2.2.8                          
## [20] LRBaseDbi_2.5.0                        
## [21] AnnotationHub_3.3.0                    
## [22] BiocFileCache_2.3.0                    
## [23] dbplyr_2.1.1                           
## [24] BiocGenerics_0.41.0                    
## [25] BiocStyle_2.23.0                       
## 
## loaded via a namespace (and not attached):
##   [1] ica_1.0-2                     Rsamtools_2.11.0             
##   [3] foreach_1.5.1                 lmtest_0.9-38                
##   [5] crayon_1.4.1                  spatstat.core_2.3-0          
##   [7] MASS_7.3-54                   nlme_3.1-153                 
##   [9] backports_1.3.0               GOSemSim_2.21.0              
##  [11] MeSHDbi_1.31.0                rlang_0.4.12                 
##  [13] XVector_0.35.0                ROCR_1.0-11                  
##  [15] irlba_2.3.3                   nnTensor_1.1.5               
##  [17] filelock_1.0.2                GOstats_2.61.0               
##  [19] BiocParallel_1.29.0           rjson_0.2.20                 
##  [21] tagcloud_0.6                  bit64_4.0.5                  
##  [23] glue_1.4.2                    sctransform_0.3.2            
##  [25] parallel_4.2.0                spatstat.sparse_2.0-0        
##  [27] dotCall64_1.0-1               tcltk_4.2.0                  
##  [29] DOSE_3.21.0                   spatstat.geom_2.3-0          
##  [31] tidyselect_1.1.1              SeuratObject_4.0.2           
##  [33] fitdistrplus_1.1-6            XML_3.99-0.8                 
##  [35] tidyr_1.1.4                   zoo_1.8-9                    
##  [37] GenomicAlignments_1.31.0      xtable_1.8-4                 
##  [39] magrittr_2.0.1                evaluate_0.14                
##  [41] ggplot2_3.3.5                 zlibbioc_1.41.0              
##  [43] miniUI_0.1.1.1                bslib_0.3.1                  
##  [45] rpart_4.1-15                  fastmatch_1.1-3              
##  [47] treeio_1.19.0                 maps_3.4.0                   
##  [49] fields_12.5                   shiny_1.7.1                  
##  [51] xfun_0.27                     cluster_2.1.2                
##  [53] tidygraph_1.2.0               TSP_1.1-11                   
##  [55] KEGGREST_1.35.0               tibble_3.1.5                 
##  [57] interactiveDisplayBase_1.33.0 ggrepel_0.9.1                
##  [59] ape_5.5                       listenv_0.8.0                
##  [61] dendextend_1.15.1             Biostrings_2.63.0            
##  [63] png_0.1-7                     future_1.22.1                
##  [65] withr_2.4.2                   bitops_1.0-7                 
##  [67] ggforce_0.3.3                 RBGL_1.71.0                  
##  [69] plyr_1.8.6                    GSEABase_1.57.0              
##  [71] pillar_1.6.4                  cachem_1.0.6                 
##  [73] graphite_1.41.0               vctrs_0.3.8                  
##  [75] ellipsis_0.3.2                generics_0.1.1               
##  [77] plot3D_1.4                    outliers_0.14                
##  [79] tools_4.2.0                   entropy_1.3.1                
##  [81] munsell_0.5.0                 tweenr_1.0.2                 
##  [83] fgsea_1.21.0                  DelayedArray_0.21.0          
##  [85] fastmap_1.1.0                 compiler_4.2.0               
##  [87] abind_1.4-5                   httpuv_1.6.3                 
##  [89] rtracklayer_1.55.0            plotly_4.10.0                
##  [91] GenomeInfoDbData_1.2.7        gridExtra_2.3                
##  [93] lattice_0.20-45               deldir_1.0-6                 
##  [95] visNetwork_2.1.0              AnnotationForge_1.37.0       
##  [97] utf8_1.2.2                    later_1.3.0                  
##  [99] dplyr_1.0.7                   jsonlite_1.7.2               
## [101] ccTensor_1.0.2                concaveman_1.1.0             
## [103] scales_1.1.1                  graph_1.73.0                 
## [105] tidytree_0.3.5                pbapply_1.5-0                
## [107] genefilter_1.77.0             lazyeval_0.2.2               
## [109] promises_1.2.0.1              goftest_1.2-3                
## [111] spatstat.utils_2.2-0          reticulate_1.22              
## [113] checkmate_2.0.0               rmarkdown_2.11               
## [115] cowplot_1.1.1                 schex_1.9.0                  
## [117] webshot_0.5.2                 Rtsne_0.15                   
## [119] uwot_0.1.10                   igraph_1.2.7                 
## [121] survival_3.2-13               yaml_2.2.1                   
## [123] plotrix_3.8-2                 htmltools_0.5.2              
## [125] memoise_2.0.0                 rTensor_1.4.8                
## [127] BiocIO_1.5.0                  Seurat_4.0.5                 
## [129] seriation_1.3.1               graphlayouts_0.7.1           
## [131] viridisLite_0.4.0             digest_0.6.28                
## [133] assertthat_0.2.1              ReactomePA_1.39.0            
## [135] mime_0.12                     rappdirs_0.3.3               
## [137] registry_0.5-1                spam_2.7-0                   
## [139] yulab.utils_0.0.4             future.apply_1.8.1           
## [141] misc3d_0.9-1                  data.table_1.14.2            
## [143] blob_1.2.2                    splines_4.2.0                
## [145] RCurl_1.98-1.5                hms_1.1.1                    
## [147] colorspace_2.0-2              BiocManager_1.30.16          
## [149] aplot_0.1.1                   sass_0.4.0                   
## [151] Rcpp_1.0.7                    bookdown_0.24                
## [153] RANN_2.6.1                    enrichplot_1.15.0            
## [155] fansi_0.5.0                   parallelly_1.28.1            
## [157] R6_2.5.1                      grid_4.2.0                   
## [159] ggridges_0.5.3                lifecycle_1.0.1              
## [161] curl_4.3.2                    leiden_0.3.9                 
## [163] meshr_2.1.0                   jquerylib_0.1.4              
## [165] DO.db_2.9                     Matrix_1.3-4                 
## [167] qvalue_2.27.0                 RcppAnnoy_0.0.19             
## [169] RColorBrewer_1.1-2            iterators_1.0.13             
## [171] stringr_1.4.0                 htmlwidgets_1.5.4            
## [173] polyclip_1.10-0               biomaRt_2.51.0               
## [175] purrr_0.3.4                   shadowtext_0.0.9             
## [177] gridGraphics_0.5-1            reactome.db_1.77.0           
## [179] mgcv_1.8-38                   globals_0.14.0               
## [181] patchwork_1.1.1               codetools_0.2-18             
## [183] prettyunits_1.1.1             gtable_0.3.0                 
## [185] DBI_1.1.1                     ggfun_0.0.4                  
## [187] tensor_1.5                    httr_1.4.2                   
## [189] highr_0.9                     KernSmooth_2.23-20           
## [191] stringi_1.7.5                 progress_1.2.2               
## [193] msigdbr_7.4.1                 reshape2_1.4.4               
## [195] farver_2.1.0                  heatmaply_1.3.0              
## [197] annotate_1.73.0               viridis_0.6.2                
## [199] hexbin_1.28.2                 fdrtool_1.2.16               
## [201] Rgraphviz_2.39.0              magick_2.7.3                 
## [203] ggtree_3.3.0                  xml2_1.3.2                   
## [205] restfulr_0.0.13               ggplotify_0.1.0              
## [207] Category_2.61.0               scattermore_0.7              
## [209] BiocVersion_3.15.0            bit_4.0.4                    
## [211] scatterpie_0.1.7              spatstat.data_2.1-0          
## [213] ggraph_2.0.5                  babelgene_21.4               
## [215] pkgconfig_2.0.3               knitr_1.36