Contents

1 Introduction

Here, we explain the way to generate CCI simulation data. scTensor has a function cellCellSimulate to generate the simulation data.

The simplest way to generate such data is cellCellSimulate with default parameters.

suppressPackageStartupMessages(library("scTensor"))
sim <- cellCellSimulate()
## Getting the values of params...
## Setting random seed...
## Generating simulation data...
## Done!

This function internally generate the parameter sets by newCCSParams, and the values of the parameter can be changed, and specified as the input of cellCellSimulate by users as follows.

# Default parameters
params <- newCCSParams()
str(params)
## Formal class 'CCSParams' [package "scTensor"] with 5 slots
##   ..@ nGene  : num 1000
##   ..@ nCell  : num [1:3] 50 50 50
##   ..@ cciInfo:List of 4
##   .. ..$ nPair: num 500
##   .. ..$ CCI1 :List of 4
##   .. .. ..$ LPattern: num [1:3] 1 0 0
##   .. .. ..$ RPattern: num [1:3] 0 1 0
##   .. .. ..$ nGene   : num 50
##   .. .. ..$ fc      : chr "E10"
##   .. ..$ CCI2 :List of 4
##   .. .. ..$ LPattern: num [1:3] 0 1 0
##   .. .. ..$ RPattern: num [1:3] 0 0 1
##   .. .. ..$ nGene   : num 50
##   .. .. ..$ fc      : chr "E10"
##   .. ..$ CCI3 :List of 4
##   .. .. ..$ LPattern: num [1:3] 0 0 1
##   .. .. ..$ RPattern: num [1:3] 1 0 0
##   .. .. ..$ nGene   : num 50
##   .. .. ..$ fc      : chr "E10"
##   ..@ lambda : num 1
##   ..@ seed   : num 1234
# Setting different parameters
# No. of genes : 1000
setParam(params, "nGene") <- 1000
# 3 cell types, 20 cells in each cell type
setParam(params, "nCell") <- c(20, 20, 20)
# Setting for Ligand-Receptor pair list
setParam(params, "cciInfo") <- list(
    nPair=500, # Total number of L-R pairs
    # 1st CCI
    CCI1=list(
        LPattern=c(1,0,0), # Only 1st cell type has this pattern
        RPattern=c(0,1,0), # Only 2nd cell type has this pattern
        nGene=50, # 50 pairs are generated as CCI1
        fc="E10"), # Degree of differential expression (Fold Change)
    # 2nd CCI
    CCI2=list(
        LPattern=c(0,1,0),
        RPattern=c(0,0,1),
        nGene=30,
        fc="E100")
    )
# Degree of Dropout
setParam(params, "lambda") <- 10
# Random number seed
setParam(params, "seed") <- 123

# Simulation data
sim <- cellCellSimulate(params)
## Getting the values of params...
## Setting random seed...
## Generating simulation data...
## Done!

The output object sim has some attributes as follows.

Firstly, sim$input contains a synthetic gene expression matrix. The size can be changed by nGene and nCell parameters described above.

dim(sim$input)
## [1] 1000   60
sim$input[1:2,1:3]
##       Cell1 Cell2 Cell3
## Gene1  9105     2     0
## Gene2     4    37   850

Next, sim$LR contains a ligand-receptor (L-R) pair list. The size can be changed by nPair parameter of cciInfo, and the differentially expressed (DE) L-R pairs are saved in the upper side of this matrix. Here, two DE L-R patterns are specified as cciInfo, and each number of pairs is 50 and 30, respectively.

dim(sim$LR)
## [1] 500   2
sim$LR[1:10,]
##    GENEID_L GENEID_R
## 1     Gene1   Gene81
## 2     Gene2   Gene82
## 3     Gene3   Gene83
## 4     Gene4   Gene84
## 5     Gene5   Gene85
## 6     Gene6   Gene86
## 7     Gene7   Gene87
## 8     Gene8   Gene88
## 9     Gene9   Gene89
## 10   Gene10   Gene90
sim$LR[46:55,]
##    GENEID_L GENEID_R
## 46   Gene46  Gene126
## 47   Gene47  Gene127
## 48   Gene48  Gene128
## 49   Gene49  Gene129
## 50   Gene50  Gene130
## 51   Gene51  Gene131
## 52   Gene52  Gene132
## 53   Gene53  Gene133
## 54   Gene54  Gene134
## 55   Gene55  Gene135
sim$LR[491:500,]
##     GENEID_L GENEID_R
## 491  Gene571  Gene991
## 492  Gene572  Gene992
## 493  Gene573  Gene993
## 494  Gene574  Gene994
## 495  Gene575  Gene995
## 496  Gene576  Gene996
## 497  Gene577  Gene997
## 498  Gene578  Gene998
## 499  Gene579  Gene999
## 500  Gene580 Gene1000

Finally, sim$celltypes contains a cell type vector. Since nCell is specified as “c(20, 20, 20)” described above, three cell types are generated.

length(sim$celltypes)
## [1] 60
head(sim$celltypes)
## Celltype1 Celltype1 Celltype1 Celltype1 Celltype1 Celltype1 
##   "Cell1"   "Cell2"   "Cell3"   "Cell4"   "Cell5"   "Cell6"
table(names(sim$celltypes))
## 
## Celltype1 Celltype2 Celltype3 
##        20        20        20

Session information

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
## 
## 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_1.20.0                          
##  [2] Homo.sapiens_1.3.1                     
##  [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
##  [4] org.Hs.eg.db_3.20.0                    
##  [5] GO.db_3.20.0                           
##  [6] OrganismDbi_1.48.0                     
##  [7] GenomicFeatures_1.58.0                 
##  [8] AnnotationDbi_1.68.0                   
##  [9] SingleCellExperiment_1.28.0            
## [10] SummarizedExperiment_1.36.0            
## [11] Biobase_2.66.0                         
## [12] GenomicRanges_1.58.0                   
## [13] GenomeInfoDb_1.42.0                    
## [14] IRanges_2.40.0                         
## [15] S4Vectors_0.44.0                       
## [16] MatrixGenerics_1.18.0                  
## [17] matrixStats_1.4.1                      
## [18] scTensor_2.16.0                        
## [19] RSQLite_2.3.7                          
## [20] LRBaseDbi_2.16.0                       
## [21] AnnotationHub_3.14.0                   
## [22] BiocFileCache_2.14.0                   
## [23] dbplyr_2.5.0                           
## [24] BiocGenerics_0.52.0                    
## [25] BiocStyle_2.34.0                       
## 
## loaded via a namespace (and not attached):
##   [1] fs_1.6.4                 bitops_1.0-9             enrichplot_1.26.0       
##   [4] httr_1.4.7               webshot_0.5.5            RColorBrewer_1.1-3      
##   [7] Rgraphviz_2.50.0         tools_4.4.1              backports_1.5.0         
##  [10] utf8_1.2.4               R6_2.5.1                 lazyeval_0.2.2          
##  [13] withr_3.0.2              prettyunits_1.2.0        graphite_1.52.0         
##  [16] gridExtra_2.3            schex_1.20.0             fdrtool_1.2.18          
##  [19] cli_3.6.3                TSP_1.2-4                entropy_1.3.1           
##  [22] sass_0.4.9               genefilter_1.88.0        meshr_2.12.0            
##  [25] Rsamtools_2.22.0         yulab.utils_0.1.7        txdbmaker_1.2.0         
##  [28] gson_0.1.0               DOSE_4.0.0               R.utils_2.12.3          
##  [31] MeSHDbi_1.42.0           AnnotationForge_1.48.0   nnTensor_1.3.0          
##  [34] plotrix_3.8-4            maps_3.4.2               visNetwork_2.1.2        
##  [37] generics_0.1.3           gridGraphics_0.5-1       GOstats_2.72.0          
##  [40] BiocIO_1.16.0            dplyr_1.1.4              dendextend_1.18.1       
##  [43] Matrix_1.7-1             fansi_1.0.6              abind_1.4-8             
##  [46] R.methodsS3_1.8.2        lifecycle_1.0.4          yaml_2.3.10             
##  [49] qvalue_2.38.0            SparseArray_1.6.0        grid_4.4.1              
##  [52] blob_1.2.4               misc3d_0.9-1             crayon_1.5.3            
##  [55] ggtangle_0.0.3           lattice_0.22-6           msigdbr_7.5.1           
##  [58] cowplot_1.1.3            annotate_1.84.0          KEGGREST_1.46.0         
##  [61] magick_2.8.5             pillar_1.9.0             knitr_1.48              
##  [64] fgsea_1.32.0             tcltk_4.4.1              rjson_0.2.23            
##  [67] codetools_0.2-20         fastmatch_1.1-4          glue_1.8.0              
##  [70] outliers_0.15            ggfun_0.1.7              data.table_1.16.2       
##  [73] vctrs_0.6.5              png_0.1-8                treeio_1.30.0           
##  [76] spam_2.11-0              rTensor_1.4.8            gtable_0.3.6            
##  [79] assertthat_0.2.1         cachem_1.1.0             xfun_0.48               
##  [82] S4Arrays_1.6.0           mime_0.12                tidygraph_1.3.1         
##  [85] survival_3.7-0           seriation_1.5.6          iterators_1.0.14        
##  [88] tinytex_0.53             fields_16.3              nlme_3.1-166            
##  [91] Category_2.72.0          ggtree_3.14.0            bit64_4.5.2             
##  [94] progress_1.2.3           filelock_1.0.3           bslib_0.8.0             
##  [97] colorspace_2.1-1         DBI_1.2.3                tidyselect_1.2.1        
## [100] bit_4.5.0                compiler_4.4.1           curl_5.2.3              
## [103] httr2_1.0.5              graph_1.84.0             xml2_1.3.6              
## [106] DelayedArray_0.32.0      plotly_4.10.4            bookdown_0.41           
## [109] rtracklayer_1.66.0       checkmate_2.3.2          scales_1.3.0            
## [112] hexbin_1.28.4            RBGL_1.82.0              plot3D_1.4.1            
## [115] rappdirs_0.3.3           stringr_1.5.1            digest_0.6.37           
## [118] rmarkdown_2.28           ca_0.71.1                XVector_0.46.0          
## [121] htmltools_0.5.8.1        pkgconfig_2.0.3          highr_0.11              
## [124] fastmap_1.2.0            rlang_1.1.4              htmlwidgets_1.6.4       
## [127] UCSC.utils_1.2.0         farver_2.1.2             jquerylib_0.1.4         
## [130] jsonlite_1.8.9           BiocParallel_1.40.0      GOSemSim_2.32.0         
## [133] R.oo_1.26.0              RCurl_1.98-1.16          magrittr_2.0.3          
## [136] GenomeInfoDbData_1.2.13  ggplotify_0.1.2          dotCall64_1.2           
## [139] patchwork_1.3.0          munsell_0.5.1            Rcpp_1.0.13             
## [142] babelgene_22.9           ape_5.8                  viridis_0.6.5           
## [145] stringi_1.8.4            tagcloud_0.6             ggraph_2.2.1            
## [148] zlibbioc_1.52.0          MASS_7.3-61              plyr_1.8.9              
## [151] parallel_4.4.1           ggrepel_0.9.6            Biostrings_2.74.0       
## [154] graphlayouts_1.2.0       splines_4.4.1            hms_1.1.3               
## [157] igraph_2.1.1             biomaRt_2.62.0           reshape2_1.4.4          
## [160] BiocVersion_3.20.0       XML_3.99-0.17            evaluate_1.0.1          
## [163] BiocManager_1.30.25      foreach_1.5.2            tweenr_2.0.3            
## [166] tidyr_1.3.1              purrr_1.0.2              polyclip_1.10-7         
## [169] heatmaply_1.5.0          ggplot2_3.5.1            ReactomePA_1.50.0       
## [172] ggforce_0.4.2            xtable_1.8-4             restfulr_0.0.15         
## [175] reactome.db_1.89.0       tidytree_0.4.6           viridisLite_0.4.2       
## [178] tibble_3.2.1             aplot_0.2.3              ccTensor_1.0.2          
## [181] GenomicAlignments_1.42.0 memoise_2.0.1            registry_0.5-1          
## [184] cluster_2.1.6            concaveman_1.1.0         GSEABase_1.68.0