Getting started with SimBu

Alexander Dietrich

Installation

To install the developmental version of the package, run:

install.packages("devtools")
devtools::install_github("omnideconv/SimBu")

To install from Bioconductor:

if (!require("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}

BiocManager::install("SimBu")
library(SimBu)

Introduction

As complex tissues are typically composed of various cell types, deconvolution tools have been developed to computationally infer their cellular composition from bulk RNA sequencing (RNA-seq) data. To comprehensively assess deconvolution performance, gold-standard datasets are indispensable. Gold-standard, experimental techniques like flow cytometry or immunohistochemistry are resource-intensive and cannot be systematically applied to the numerous cell types and tissues profiled with high-throughput transcriptomics. The simulation of ‘pseudo-bulk’ data, generated by aggregating single-cell RNA-seq (scRNA-seq) expression profiles in pre-defined proportions, offers a scalable and cost-effective alternative. This makes it feasible to create in silico gold standards that allow fine-grained control of cell-type fractions not conceivable in an experimental setup. However, at present, no simulation software for generating pseudo-bulk RNA-seq data exists.
SimBu was developed to simulate pseudo-bulk samples based on various simulation scenarios, designed to test specific features of deconvolution methods. A unique feature of SimBu is the modelling of cell-type-specific mRNA bias using experimentally-derived or data-driven scaling factors. Here, we show that SimBu can generate realistic pseudo-bulk data, recapitulating the biological and statistical features of real RNA-seq data. Finally, we illustrate the impact of mRNA bias on the evaluation of deconvolution tools and provide recommendations for the selection of suitable methods for estimating mRNA content.

Getting started

This chapter covers all you need to know to quickly simulate some pseudo-bulk samples!

This package can simulate samples from local or public data. This vignette will work with artificially generated data as it serves as an overview for the features implemented in SimBu. For the public data integration using sfaira (Fischer et al. 2020), please refer to the “Public Data Integration” vignette.

We will create some toy data to use for our simulations; two matrices with 300 cells each and 1000 genes/features. One represents raw count data, while the other matrix represents scaled TPM-like data. We will assign these cells to some immune cell types.

counts <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE)
tpm <- Matrix::Matrix(matrix(stats::rpois(3e5, 5), ncol = 300), sparse = TRUE)
tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))
colnames(counts) <- paste0("cell_", rep(1:300))
colnames(tpm) <- paste0("cell_", rep(1:300))
rownames(counts) <- paste0("gene_", rep(1:1000))
rownames(tpm) <- paste0("gene_", rep(1:1000))
annotation <- data.frame(
  "ID" = paste0("cell_", rep(1:300)),
  "cell_type" = c(
    rep("T cells CD4", 50),
    rep("T cells CD8", 50),
    rep("Macrophages", 100),
    rep("NK cells", 10),
    rep("B cells", 70),
    rep("Monocytes", 20)
  )
)

Creating a dataset

SimBu uses the SummarizedExperiment class as storage for count data as well as annotation data. Currently it is possible to store two matrices at the same time: raw counts and TPM-like data (this can also be some other scaled count matrix, such as RPKM, but we recommend to use TPMs). These two matrices have to have the same dimensions and have to contain the same genes and cells. Providing the raw count data is mandatory!
SimBu scales the matrix that is added via the tpm_matrix slot by default to 1e6 per cell, if you do not want this, you can switch it off by setting the scale_tpm parameter to FALSE. Additionally, the cell type annotation of the cells has to be given in a dataframe, which has to include the two columns ID and cell_type. If additional columns from this annotation should be transferred to the dataset, simply give the names of them in the additional_cols parameter.

To generate a dataset that can be used in SimBu, you can use the dataset() method; other methods exist as well, which are covered in the “Inputs & Outputs” vignette.

ds <- SimBu::dataset(
  annotation = annotation,
  count_matrix = counts,
  tpm_matrix = tpm,
  name = "test_dataset"
)
#> Filtering genes...
#> Created dataset.

SimBu offers basic filtering options for your dataset, which you can apply during dataset generation:

Simulate pseudo bulk datasets

We are now ready to simulate the first pseudo bulk samples with the created dataset:

simulation <- SimBu::simulate_bulk(
  data = ds,
  scenario = "random",
  scaling_factor = "NONE",
  ncells = 100,
  nsamples = 10,
  BPPARAM = BiocParallel::MulticoreParam(workers = 4), # this will use 4 threads to run the simulation
  run_parallel = TRUE
) # multi-threading to TRUE
#> Using parallel generation of simulations.
#> Warning in BiocParallel::MulticoreParam(workers = 4): MulticoreParam() not
#> supported on Windows, use SnowParam()
#> Finished simulation.

ncells sets the number of cells in each sample, while nsamples sets the total amount of simulated samples.
If you want to simulate a specific sequencing depth in your simulations, you can use the total_read_counts parameter to do so. Note that this parameter is only applied on the counts matrix (if supplied), as TPMs will be scaled to 1e6 by default.

SimBu can add mRNA bias by using different scaling factors to the simulations using the scaling_factor parameter. A detailed explanation can be found in the “Scaling factor” vignette.

Currently there are 6 scenarios implemented in the package:

pure_scenario_dataframe <- data.frame(
  "B cells" = c(0.2, 0.1, 0.5, 0.3),
  "T cells" = c(0.3, 0.8, 0.2, 0.5),
  "NK cells" = c(0.5, 0.1, 0.3, 0.2),
  row.names = c("sample1", "sample2", "sample3", "sample4")
)
pure_scenario_dataframe
#>         B.cells T.cells NK.cells
#> sample1     0.2     0.3      0.5
#> sample2     0.1     0.8      0.1
#> sample3     0.5     0.2      0.3
#> sample4     0.3     0.5      0.2

Results

The simulation object contains three named entries:

utils::head(SummarizedExperiment::assays(simulation$bulk)[["bulk_counts"]])
#> 6 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names 'random_sample1', 'random_sample2', 'random_sample3' ... ]]
#>                                               
#> gene_1 477 475 509 478 498 454 480 500 464 496
#> gene_2 495 521 506 559 569 543 535 569 522 572
#> gene_3 538 494 483 538 511 520 495 534 463 502
#> gene_4 465 446 487 498 465 487 513 498 503 483
#> gene_5 493 516 486 498 528 465 528 502 461 498
#> gene_6 575 484 521 532 524 546 521 502 477 556
utils::head(SummarizedExperiment::assays(simulation$bulk)[["bulk_tpm"]])
#> 6 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names 'random_sample1', 'random_sample2', 'random_sample3' ... ]]
#>                                                                            
#> gene_1  975.9358  976.0042 1033.9208 981.3322  933.6119  968.5616  953.0302
#> gene_2  953.0462  937.6816  953.9691 885.9947  931.1020  914.2038  945.2205
#> gene_3 1057.3274 1006.1676 1024.7467 959.1410 1071.6460 1009.1044 1006.1770
#> gene_4  988.5584 1050.7465  965.3665 992.0771  975.1270 1057.6656 1034.9350
#> gene_5  950.7621  997.3894  970.0523 993.9822 1078.1963 1043.7981  969.3079
#> gene_6  930.8510  937.0937  990.8827 938.0625  876.3442  998.3519  919.2534
#>                                    
#> gene_1  994.4791  913.3561 942.6171
#> gene_2  905.4779  910.5348 902.7957
#> gene_3  977.2147  892.0189 919.8009
#> gene_4  998.4379  999.3079 914.7519
#> gene_5 1051.7827 1009.2038 994.5759
#> gene_6  877.4617  910.9563 875.2130

If only a single matrix was given to the dataset initially, only one assay is filled.

It is also possible to merge simulations:

simulation2 <- SimBu::simulate_bulk(
  data = ds,
  scenario = "even",
  scaling_factor = "NONE",
  ncells = 1000,
  nsamples = 10,
  BPPARAM = BiocParallel::MulticoreParam(workers = 4),
  run_parallel = TRUE
)
#> Using parallel generation of simulations.
#> Warning in BiocParallel::MulticoreParam(workers = 4): MulticoreParam() not
#> supported on Windows, use SnowParam()
#> Finished simulation.
merged_simulations <- SimBu::merge_simulations(list(simulation, simulation2))

Finally here is a barplot of the resulting simulation:

SimBu::plot_simulation(simulation = merged_simulations)

More features

Simulate using a whitelist (and blacklist) of cell-types

Sometimes, you are only interested in specific cell-types (for example T cells), but the dataset you are using has too many other cell-types; you can handle this issue during simulation using the whitelist parameter:

simulation <- SimBu::simulate_bulk(
  data = ds,
  scenario = "random",
  scaling_factor = "NONE",
  ncells = 1000,
  nsamples = 20,
  BPPARAM = BiocParallel::MulticoreParam(workers = 4),
  run_parallel = TRUE,
  whitelist = c("T cells CD4", "T cells CD8")
)
#> Using parallel generation of simulations.
#> Warning in BiocParallel::MulticoreParam(workers = 4): MulticoreParam() not
#> supported on Windows, use SnowParam()
#> Finished simulation.
SimBu::plot_simulation(simulation = simulation)

In the same way, you can also provide a blacklist parameter, where you name the cell-types you don’t want to be included in your simulation.

utils::sessionInfo()
#> R version 4.3.2 (2023-10-31 ucrt)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows Server 2022 x64 (build 20348)
#> 
#> Matrix products: default
#> 
#> 
#> locale:
#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.utf8   
#> [3] LC_MONETARY=English_United States.utf8
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.utf8    
#> 
#> time zone: America/New_York
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] SimBu_1.4.3
#> 
#> loaded via a namespace (and not attached):
#>  [1] SummarizedExperiment_1.32.0 gtable_0.3.4               
#>  [3] xfun_0.41                   bslib_0.6.1                
#>  [5] ggplot2_3.4.4               Biobase_2.62.0             
#>  [7] lattice_0.22-5              vctrs_0.6.5                
#>  [9] tools_4.3.2                 bitops_1.0-7               
#> [11] generics_0.1.3              stats4_4.3.2               
#> [13] parallel_4.3.2              tibble_3.2.1               
#> [15] fansi_1.0.6                 highr_0.10                 
#> [17] pkgconfig_2.0.3             Matrix_1.6-4               
#> [19] data.table_1.14.10          RColorBrewer_1.1-3         
#> [21] S4Vectors_0.40.2            sparseMatrixStats_1.14.0   
#> [23] RcppParallel_5.1.7          lifecycle_1.0.4            
#> [25] GenomeInfoDbData_1.2.11     farver_2.1.1               
#> [27] compiler_4.3.2              munsell_0.5.0              
#> [29] codetools_0.2-19            GenomeInfoDb_1.38.3        
#> [31] htmltools_0.5.7             sass_0.4.8                 
#> [33] RCurl_1.98-1.13             yaml_2.3.8                 
#> [35] pillar_1.9.0                crayon_1.5.2               
#> [37] jquerylib_0.1.4             tidyr_1.3.0                
#> [39] BiocParallel_1.36.0         DelayedArray_0.28.0        
#> [41] cachem_1.0.8                abind_1.4-5                
#> [43] tidyselect_1.2.0            digest_0.6.33              
#> [45] dplyr_1.1.4                 purrr_1.0.2                
#> [47] labeling_0.4.3              fastmap_1.1.1              
#> [49] grid_4.3.2                  colorspace_2.1-0           
#> [51] cli_3.6.2                   SparseArray_1.2.2          
#> [53] magrittr_2.0.3              S4Arrays_1.2.0             
#> [55] utf8_1.2.4                  withr_2.5.2                
#> [57] scales_1.3.0                rmarkdown_2.25             
#> [59] XVector_0.42.0              matrixStats_1.2.0          
#> [61] proxyC_0.3.4                evaluate_0.23              
#> [63] knitr_1.45                  GenomicRanges_1.54.1       
#> [65] IRanges_2.36.0              rlang_1.1.2                
#> [67] Rcpp_1.0.11                 glue_1.6.2                 
#> [69] BiocGenerics_0.48.1         jsonlite_1.8.8             
#> [71] R6_2.5.1                    MatrixGenerics_1.14.0      
#> [73] zlibbioc_1.48.0

References

Fischer, David S., Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Sophie Tritschler, Olle Holmberg, Hananeh Aliee, and Fabian J. Theis. 2020. “Sfaira Accelerates Data and Model Reuse in Single Cell Genomics.” bioRxiv. https://doi.org/10.1101/2020.12.16.419036.