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$bulk)[["bulk_counts"]])
#> 6 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names 'random_sample1', 'random_sample2', 'random_sample3' ... ]]
#>                                               
#> gene_1 502 507 492 505 548 497 492 508 545 522
#> gene_2 486 490 429 494 516 466 468 470 492 473
#> gene_3 438 439 458 458 482 456 507 477 456 496
#> gene_4 518 536 532 482 487 490 513 505 491 462
#> gene_5 503 496 496 497 483 451 477 475 521 502
#> gene_6 472 479 472 431 508 490 484 476 534 527
utils::head(SummarizedExperiment::assays(simulation$bulk)[["bulk_tpm"]])
#> 6 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names 'random_sample1', 'random_sample2', 'random_sample3' ... ]]
#>                                                                            
#> gene_1 1004.5305 1032.9953  973.8969  920.8519 1020.600  959.5680  977.5492
#> gene_2  987.3581 1022.4010  957.3279 1037.1603 1045.305 1064.3281  951.2472
#> gene_3 1039.4795 1133.8820 1085.4016  996.0905 1118.750 1045.0502 1021.0422
#> gene_4  990.5873 1076.0288  996.2860  971.2512 1053.531  957.4139  955.7714
#> gene_5  956.3105  961.0124 1103.1500 1091.1941 1001.897 1166.4258 1039.1785
#> gene_6 1070.7336  953.8982  976.0942 1006.0803 1009.892 1054.2855  954.1629
#>                                     
#> gene_1  887.0925 1007.9648  966.1126
#> gene_2 1069.8397  928.1424 1086.9995
#> gene_3 1080.9772 1057.0903 1020.2131
#> gene_4  975.1950 1020.9855  995.3631
#> gene_5 1022.3105  959.4561 1074.1162
#> gene_6 1058.5789  997.4767 1082.0621

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 4.4.0 RC (2024-04-16 r86468 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> 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_1.7.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] SummarizedExperiment_1.35.0 gtable_0.3.5               
#>  [3] xfun_0.43                   bslib_0.7.0                
#>  [5] ggplot2_3.5.1               Biobase_2.65.0             
#>  [7] lattice_0.22-6              vctrs_0.6.5                
#>  [9] tools_4.4.0                 generics_0.1.3             
#> [11] stats4_4.4.0                parallel_4.4.0             
#> [13] tibble_3.2.1                fansi_1.0.6                
#> [15] highr_0.10                  pkgconfig_2.0.3            
#> [17] Matrix_1.7-0                data.table_1.15.4          
#> [19] RColorBrewer_1.1-3          S4Vectors_0.43.0           
#> [21] sparseMatrixStats_1.17.0    lifecycle_1.0.4            
#> [23] GenomeInfoDbData_1.2.12     compiler_4.4.0             
#> [25] farver_2.1.1                munsell_0.5.1              
#> [27] codetools_0.2-20            GenomeInfoDb_1.41.0        
#> [29] htmltools_0.5.8.1           sass_0.4.9                 
#> [31] yaml_2.3.8                  pillar_1.9.0               
#> [33] crayon_1.5.2                jquerylib_0.1.4            
#> [35] tidyr_1.3.1                 BiocParallel_1.39.0        
#> [37] DelayedArray_0.31.0         cachem_1.0.8               
#> [39] abind_1.4-5                 tidyselect_1.2.1           
#> [41] digest_0.6.35               dplyr_1.1.4                
#> [43] purrr_1.0.2                 labeling_0.4.3             
#> [45] fastmap_1.1.1               grid_4.4.0                 
#> [47] colorspace_2.1-0            cli_3.6.2                  
#> [49] SparseArray_1.5.0           magrittr_2.0.3             
#> [51] S4Arrays_1.5.0              utf8_1.2.4                 
#> [53] withr_3.0.0                 UCSC.utils_1.1.0           
#> [55] scales_1.3.0                rmarkdown_2.26             
#> [57] XVector_0.45.0              httr_1.4.7                 
#> [59] matrixStats_1.3.0           proxyC_0.4.1               
#> [61] evaluate_0.23               knitr_1.46                 
#> [63] GenomicRanges_1.57.0        IRanges_2.39.0             
#> [65] rlang_1.1.3                 Rcpp_1.0.12                
#> [67] glue_1.7.0                  BiocGenerics_0.51.0        
#> [69] jsonlite_1.8.8              R6_2.5.1                   
#> [71] MatrixGenerics_1.17.0       zlibbioc_1.51.0

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.