Performing scClassify using pretrained model
25 April 2023
1 Introduction
A common application of single-cell RNA sequencing (RNA-seq) data is
to identify discrete cell types. To take advantage of the large collection
of well-annotated scRNA-seq datasets, scClassify package implements
a set of methods to perform accurate cell type classification based on
ensemble learning and sample size calculation.
This vignette will provide an example showing how users can use a pretrained
model of scClassify to predict cell types. A pretrained model is a
scClassifyTrainModel object returned by train_scClassify().
A list of pretrained model can be found in
https://sydneybiox.github.io/scClassify/index.html.
First, install scClassify, install BiocManager and use
BiocManager::install to install scClassify package.
# installation of scClassify
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("scClassify")2 Setting up the data
We assume that you have log-transformed (size-factor normalized) matrices as query datasets, where each row refers to a gene and each column a cell. For demonstration purposes, we will take a subset of single-cell pancreas datasets from one independent study (Wang et al.).
library(scClassify)
data("scClassify_example")
wang_cellTypes <- scClassify_example$wang_cellTypes
exprsMat_wang_subset <- scClassify_example$exprsMat_wang_subset
exprsMat_wang_subset <- as(exprsMat_wang_subset, "dgCMatrix")Here, we load our pretrained model using a subset of the Xin et al. human pancreas dataset as our reference data.
First, let us check basic information relating to our pretrained model.
data("trainClassExample_xin")
trainClassExample_xin
#> Class: scClassifyTrainModel
#> Model name: training
#> Feature selection methods: limma
#> Number of cells in the training data: 674
#> Number of cell types in the training data: 4In this pretrained model, we have selected the genes based on Differential Expression using limma. To check the genes that are available in the pretrained model:
features(trainClassExample_xin)
#> [1] "limma"We can also visualise the cell type tree of the reference data.
plotCellTypeTree(cellTypeTree(trainClassExample_xin))
3 Running scClassify
Next, we perform predict_scClassify with our pretrained model
trainRes = trainClassExample to predict the cell types of our
query data matrix exprsMat_wang_subset_sparse. Here,
we used pearson and spearman as similarity metrics.
pred_res <- predict_scClassify(exprsMat_test = exprsMat_wang_subset,
trainRes = trainClassExample_xin,
cellTypes_test = wang_cellTypes,
algorithm = "WKNN",
features = c("limma"),
similarity = c("pearson", "spearman"),
prob_threshold = 0.7,
verbose = TRUE)
#> Performing unweighted ensemble learning...
#> Using parameters:
#> similarity algorithm features
#> "pearson" "WKNN" "limma"
#> [1] "Using dynamic correlation cutoff..."
#> [1] "Using dynamic correlation cutoff..."
#> classify_res
#> correct correctly unassigned intermediate
#> 0.704590818 0.239520958 0.000000000
#> incorrectly unassigned error assigned misclassified
#> 0.000000000 0.051896208 0.003992016
#> Using parameters:
#> similarity algorithm features
#> "spearman" "WKNN" "limma"
#> [1] "Using dynamic correlation cutoff..."
#> [1] "Using dynamic correlation cutoff..."
#> classify_res
#> correct correctly unassigned intermediate
#> 0.702594810 0.013972056 0.000000000
#> incorrectly unassigned error assigned misclassified
#> 0.001996008 0.277445110 0.003992016
#> weights for each base method:
#> [1] NA NANoted that the cellType_test is not a required input.
For datasets with unknown labels, users can simply leave it
as cellType_test = NULL.
Prediction results for pearson as the similarity metric:
table(pred_res$pearson_WKNN_limma$predRes, wang_cellTypes)
#> wang_cellTypes
#> acinar alpha beta delta ductal gamma stellate
#> alpha 0 206 0 0 0 2 0
#> beta 0 0 118 0 1 0 0
#> beta_delta_gamma 0 0 0 0 25 0 0
#> delta 0 0 0 10 0 0 0
#> gamma 0 0 0 0 0 19 0
#> unassigned 5 0 0 0 70 0 45Prediction results for spearman as the similarity metric:
table(pred_res$spearman_WKNN_limma$predRes, wang_cellTypes)
#> wang_cellTypes
#> acinar alpha beta delta ductal gamma stellate
#> alpha 0 206 0 0 0 2 2
#> beta 2 0 118 0 29 0 6
#> beta_delta_gamma 1 0 0 0 66 0 31
#> delta 0 0 0 10 0 0 2
#> gamma 0 0 0 0 0 18 0
#> unassigned 2 0 0 0 1 1 44 Session Info
sessionInfo()
#> R version 4.3.0 RC (2023-04-13 r84269)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.17-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] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] scClassify_1.12.0 BiocStyle_2.28.0
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 gridExtra_2.3
#> [3] rlang_1.1.0 magrittr_2.0.3
#> [5] matrixStats_0.63.0 compiler_4.3.0
#> [7] mgcv_1.8-42 DelayedMatrixStats_1.22.0
#> [9] vctrs_0.6.2 reshape2_1.4.4
#> [11] stringr_1.5.0 pkgconfig_2.0.3
#> [13] fastmap_1.1.1 magick_2.7.4
#> [15] XVector_0.40.0 labeling_0.4.2
#> [17] ggraph_2.1.0 utf8_1.2.3
#> [19] rmarkdown_2.21 purrr_1.0.1
#> [21] xfun_0.39 zlibbioc_1.46.0
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#> [29] Rhdf5lib_1.22.0 BiocParallel_1.34.0
#> [31] tweenr_2.0.2 parallel_4.3.0
#> [33] cluster_2.1.4 R6_2.5.1
#> [35] bslib_0.4.2 stringi_1.7.12
#> [37] limma_3.56.0 diptest_0.76-0
#> [39] GenomicRanges_1.52.0 jquerylib_0.1.4
#> [41] Rcpp_1.0.10 bookdown_0.33
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#> [69] BiocManager_1.30.20 MatrixGenerics_1.12.0
#> [71] stats4_4.3.0 plotly_4.10.1
#> [73] generics_0.1.3 RCurl_1.98-1.12
#> [75] S4Vectors_0.38.0 ggplot2_3.4.2
#> [77] sparseMatrixStats_1.12.0 munsell_0.5.0
#> [79] scales_1.2.1 glue_1.6.2
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#> [113] MASS_7.3-59