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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] scTGIF_1.16.0                          
##  [2] Homo.sapiens_1.3.1                     
##  [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [4] org.Hs.eg.db_3.18.0                    
##  [5] GO.db_3.18.0                           
##  [6] OrganismDbi_1.44.0                     
##  [7] GenomicFeatures_1.54.0                 
##  [8] AnnotationDbi_1.64.0                   
##  [9] SingleCellExperiment_1.24.0            
## [10] SummarizedExperiment_1.32.0            
## [11] Biobase_2.62.0                         
## [12] GenomicRanges_1.54.0                   
## [13] GenomeInfoDb_1.38.0                    
## [14] IRanges_2.36.0                         
## [15] MatrixGenerics_1.14.0                  
## [16] matrixStats_1.0.0                      
## [17] scTensor_2.12.0                        
## [18] RSQLite_2.3.1                          
## [19] LRBaseDbi_2.12.0                       
## [20] S4Vectors_0.40.0                       
## [21] AnnotationHub_3.10.0                   
## [22] BiocFileCache_2.10.0                   
## [23] dbplyr_2.3.4                           
## [24] BiocGenerics_0.48.0                    
## [25] BiocStyle_2.30.0                       
## 
## loaded via a namespace (and not attached):
##   [1] rTensor_1.4.8                 GSEABase_1.64.0              
##   [3] progress_1.2.2                goftest_1.2-3                
##   [5] Biostrings_2.70.0             vctrs_0.6.4                  
##   [7] spatstat.random_3.2-1         digest_0.6.33                
##   [9] png_0.1-8                     registry_0.5-1               
##  [11] ggrepel_0.9.4                 deldir_1.0-9                 
##  [13] parallelly_1.36.0             magick_2.8.1                 
##  [15] MASS_7.3-60                   reshape2_1.4.4               
##  [17] httpuv_1.6.12                 foreach_1.5.2                
##  [19] qvalue_2.34.0                 withr_2.5.1                  
##  [21] xfun_0.40                     ggfun_0.1.3                  
##  [23] ellipsis_0.3.2                survival_3.5-7               
##  [25] memoise_2.0.1                 hexbin_1.28.3                
##  [27] gson_0.1.0                    tidytree_0.4.5               
##  [29] zoo_1.8-12                    pbapply_1.7-2                
##  [31] entropy_1.3.1                 prettyunits_1.2.0            
##  [33] KEGGREST_1.42.0               promises_1.2.1               
##  [35] httr_1.4.7                    restfulr_0.0.15              
##  [37] schex_1.16.0                  globals_0.16.2               
##  [39] fitdistrplus_1.1-11           miniUI_0.1.1.1               
##  [41] generics_0.1.3                DOSE_3.28.0                  
##  [43] reactome.db_1.86.0            babelgene_22.9               
##  [45] concaveman_1.1.0              curl_5.1.0                   
##  [47] fields_15.2                   zlibbioc_1.48.0              
##  [49] ggraph_2.1.0                  polyclip_1.10-6              
##  [51] ca_0.71.1                     GenomeInfoDbData_1.2.11      
##  [53] SparseArray_1.2.0             RBGL_1.78.0                  
##  [55] interactiveDisplayBase_1.40.0 xtable_1.8-4                 
##  [57] stringr_1.5.0                 evaluate_0.22                
##  [59] S4Arrays_1.2.0                hms_1.1.3                    
##  [61] bookdown_0.36                 irlba_2.3.5.1                
##  [63] colorspace_2.1-0              filelock_1.0.2               
##  [65] visNetwork_2.1.2              ROCR_1.0-11                  
##  [67] reticulate_1.34.0             spatstat.data_3.0-3          
##  [69] magrittr_2.0.3                lmtest_0.9-40                
##  [71] Rgraphviz_2.46.0              later_1.3.1                  
##  [73] viridis_0.6.4                 ggtree_3.10.0                
##  [75] lattice_0.22-5                misc3d_0.9-1                 
##  [77] spatstat.geom_3.2-7           future.apply_1.11.0          
##  [79] genefilter_1.84.0             plot3D_1.4                   
##  [81] scattermore_1.2               XML_3.99-0.14                
##  [83] shadowtext_0.1.2              cowplot_1.1.1                
##  [85] RcppAnnoy_0.0.21              pillar_1.9.0                 
##  [87] nlme_3.1-163                  iterators_1.0.14             
##  [89] compiler_4.3.1                stringi_1.7.12               
##  [91] Category_2.68.0               TSP_1.2-4                    
##  [93] tensor_1.5                    dendextend_1.17.1            
##  [95] GenomicAlignments_1.38.0      MPO.db_0.99.7                
##  [97] plyr_1.8.9                    msigdbr_7.5.1                
##  [99] BiocIO_1.12.0                 crayon_1.5.2                 
## [101] abind_1.4-5                   gridGraphics_0.5-1           
## [103] sp_2.1-1                      graphlayouts_1.0.1           
## [105] bit_4.0.5                     dplyr_1.1.3                  
## [107] fastmatch_1.1-4               tagcloud_0.6                 
## [109] codetools_0.2-19              bslib_0.5.1                  
## [111] plotly_4.10.3                 mime_0.12                    
## [113] splines_4.3.1                 Rcpp_1.0.11                  
## [115] HDO.db_0.99.1                 knitr_1.44                   
## [117] blob_1.2.4                    utf8_1.2.4                   
## [119] BiocVersion_3.18.0            fs_1.6.3                     
## [121] listenv_0.9.0                 checkmate_2.2.0              
## [123] ggplotify_0.1.2               tibble_3.2.1                 
## [125] Matrix_1.6-1.1                tweenr_2.0.2                 
## [127] pkgconfig_2.0.3               tools_4.3.1                  
## [129] cachem_1.0.8                  viridisLite_0.4.2            
## [131] DBI_1.1.3                     graphite_1.48.0              
## [133] fastmap_1.1.1                 rmarkdown_2.25               
## [135] scales_1.2.1                  grid_4.3.1                   
## [137] outliers_0.15                 ica_1.0-3                    
## [139] Seurat_4.4.0                  Rsamtools_2.18.0             
## [141] sass_0.4.7                    patchwork_1.1.3              
## [143] BiocManager_1.30.22           dotCall64_1.1-0              
## [145] graph_1.80.0                  RANN_2.6.1                   
## [147] farver_2.1.1                  tidygraph_1.2.3              
## [149] scatterpie_0.2.1              yaml_2.3.7                   
## [151] AnnotationForge_1.44.0        rtracklayer_1.62.0           
## [153] cli_3.6.1                     purrr_1.0.2                  
## [155] webshot_0.5.5                 leiden_0.4.3                 
## [157] lifecycle_1.0.3               uwot_0.1.16                  
## [159] backports_1.4.1               BiocParallel_1.36.0          
## [161] annotate_1.80.0               MeSHDbi_1.38.0               
## [163] rjson_0.2.21                  gtable_0.3.4                 
## [165] ggridges_0.5.4                progressr_0.14.0             
## [167] parallel_4.3.1                ape_5.7-1                    
## [169] jsonlite_1.8.7                seriation_1.5.1              
## [171] bitops_1.0-7                  ggplot2_3.4.4                
## [173] HPO.db_0.99.2                 bit64_4.0.5                  
## [175] assertthat_0.2.1              Rtsne_0.16                   
## [177] yulab.utils_0.1.0             ReactomePA_1.46.0            
## [179] spatstat.utils_3.0-4          SeuratObject_4.1.4           
## [181] heatmaply_1.5.0               jquerylib_0.1.4              
## [183] nnTensor_1.2.0                GOSemSim_2.28.0              
## [185] ccTensor_1.0.2                lazyeval_0.2.2               
## [187] shiny_1.7.5.1                 htmltools_0.5.6.1            
## [189] enrichplot_1.22.0             sctransform_0.4.1            
## [191] rappdirs_0.3.3                glue_1.6.2                   
## [193] tcltk_4.3.1                   spam_2.10-0                  
## [195] XVector_0.42.0                RCurl_1.98-1.12              
## [197] treeio_1.26.0                 gridExtra_2.3                
## [199] igraph_1.5.1                  R6_2.5.1                     
## [201] tidyr_1.3.0                   fdrtool_1.2.17               
## [203] cluster_2.1.4                 aplot_0.2.2                  
## [205] DelayedArray_0.28.0           tidyselect_1.2.0             
## [207] plotrix_3.8-2                 GOstats_2.68.0               
## [209] maps_3.4.1                    xml2_1.3.5                   
## [211] ggforce_0.4.1                 future_1.33.0                
## [213] munsell_0.5.0                 KernSmooth_2.23-22           
## [215] data.table_1.14.8             htmlwidgets_1.6.2            
## [217] fgsea_1.28.0                  RColorBrewer_1.1-3           
## [219] biomaRt_2.58.0                rlang_1.1.1                  
## [221] spatstat.sparse_3.0-3         meshr_2.8.0                  
## [223] spatstat.explore_3.2-5        fansi_1.0.5