scds:single cell doublet scoring: In-silico doublet annotation for single cell RNA sequencing data
Introduction
In this vignette, we provide an overview of the basic functionality
and usage of the scds package, which interfaces with
SingleCellExperiment objects.
Installation
Install the scds package using Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scds", version = "3.9")Or from github:
Quick start
scds takes as input a SingleCellExperiment
object (see here SingleCellExperiment),
where raw counts are stored in a counts assay,
i.e. assay(sce,"counts"). An example dataset created by
sub-sampling the cell-hashing cell-lines data set (see https://satijalab.org/seurat/hashing_vignette.html) is
included with the package and accessible via
data("sce").Note that scds is designed to
workd with larger datasets, but for the purposes of this vignette, we
work with a smaller example dataset. We apply scds to this
data and compare/visualize reasults:
Example data set
Get example data set provided with the package.
library(scds)
library(scater)
library(rsvd)
library(Rtsne)
library(cowplot)
set.seed(30519)
data("sce_chcl")
sce = sce_chcl #- less typing
dim(sce)## [1] 2000 2000We see it contains 2,000 genes and 2,000 cells, 216 of which are identified as doublets:
##
## Doublet Negative Singlet
## 216 83 1701We can visualize cells/doublets after projecting into two dimensions:
logcounts(sce) = log1p(counts(sce))
vrs = apply(logcounts(sce),1,var)
pc = rpca(t(logcounts(sce)[order(vrs,decreasing=TRUE)[1:100],]))
ts = Rtsne(pc$x[,1:10],verb=FALSE)
reducedDim(sce,"tsne") = ts$Y; rm(ts,vrs,pc)
plotReducedDim(sce,"tsne",color_by="hto_classification_global")
Computational doublet annotation
We now run the scds doublet annotation approaches.
Briefly, we identify doublets in two complementary ways:
cxds is based on co-expression of gene pairs and works with
absence/presence calls only, while bcds uses the full count
information and a binary classification approach using artificially
generated doublets. cxds_bcds_hybrid combines both
approaches, for more details please consult (this manuscript). Each of the
three methods returns a doublet score, with higher scores indicating
more “doublet-like” barcodes.
#- Annotate doublet using co-expression based doublet scoring:
sce = cxds(sce,retRes = TRUE)
sce = bcds(sce,retRes = TRUE,verb=TRUE)
sce = cxds_bcds_hybrid(sce)
par(mfcol=c(1,3))
boxplot(sce$cxds_score ~ sce$doublet_true_labels, main="cxds")
boxplot(sce$bcds_score ~ sce$doublet_true_labels, main="bcds")
boxplot(sce$hybrid_score ~ sce$doublet_true_labels, main="hybrid")
Visualizing gene pairs
For cxds we can identify and visualize gene pairs
driving doublet annoataions, with the expectation that the two genes in
a pair might mark different types of cells (see manuscript). In the
following we look at the top three pairs, each gene pair is a row in the
plot below:
scds =
top3 = metadata(sce)$cxds$topPairs[1:3,]
rs = rownames(sce)
hb = rowData(sce)$cxds_hvg_bool
ho = rowData(sce)$cxds_hvg_ordr[hb]
hgs = rs[ho]
l1 = ggdraw() + draw_text("Pair 1", x = 0.5, y = 0.5)
p1 = plotReducedDim(sce,"tsne",color_by=hgs[top3[1,1]])
p2 = plotReducedDim(sce,"tsne",color_by=hgs[top3[1,2]])
l2 = ggdraw() + draw_text("Pair 2", x = 0.5, y = 0.5)
p3 = plotReducedDim(sce,"tsne",color_by=hgs[top3[2,1]])
p4 = plotReducedDim(sce,"tsne",color_by=hgs[top3[2,2]])
l3 = ggdraw() + draw_text("Pair 3", x = 0.5, y = 0.5)
p5 = plotReducedDim(sce,"tsne",color_by=hgs[top3[3,1]])
p6 = plotReducedDim(sce,"tsne",color_by=hgs[top3[3,2]])
plot_grid(l1,p1,p2,l2,p3,p4,l3,p5,p6,ncol=3, rel_widths = c(1,2,2))Session Info
## 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: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] cowplot_1.1.3 Rtsne_0.17
## [3] rsvd_1.0.5 scater_1.34.0
## [5] ggplot2_3.5.1 scuttle_1.16.0
## [7] SingleCellExperiment_1.28.0 SummarizedExperiment_1.36.0
## [9] Biobase_2.67.0 GenomicRanges_1.59.0
## [11] GenomeInfoDb_1.43.0 IRanges_2.41.0
## [13] S4Vectors_0.44.0 BiocGenerics_0.53.0
## [15] MatrixGenerics_1.19.0 matrixStats_1.4.1
## [17] scds_1.23.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 viridisLite_0.4.2 farver_2.1.2
## [4] dplyr_1.1.4 vipor_0.4.7 viridis_0.6.5
## [7] fastmap_1.2.0 pROC_1.18.5 digest_0.6.37
## [10] lifecycle_1.0.4 magrittr_2.0.3 compiler_4.4.1
## [13] rlang_1.1.4 sass_0.4.9 tools_4.4.1
## [16] utf8_1.2.4 yaml_2.3.10 data.table_1.16.2
## [19] knitr_1.48 labeling_0.4.3 S4Arrays_1.6.0
## [22] xgboost_1.7.8.1 DelayedArray_0.33.1 plyr_1.8.9
## [25] abind_1.4-8 BiocParallel_1.41.0 withr_3.0.2
## [28] sys_3.4.3 grid_4.4.1 fansi_1.0.6
## [31] beachmat_2.23.0 colorspace_2.1-1 scales_1.3.0
## [34] cli_3.6.3 rmarkdown_2.28 crayon_1.5.3
## [37] generics_0.1.3 httr_1.4.7 ggbeeswarm_0.7.2
## [40] cachem_1.1.0 zlibbioc_1.52.0 parallel_4.4.1
## [43] BiocManager_1.30.25 XVector_0.46.0 vctrs_0.6.5
## [46] Matrix_1.7-1 jsonlite_1.8.9 BiocSingular_1.23.0
## [49] BiocNeighbors_2.1.0 ggrepel_0.9.6 irlba_2.3.5.1
## [52] beeswarm_0.4.0 maketools_1.3.1 jquerylib_0.1.4
## [55] glue_1.8.0 codetools_0.2-20 gtable_0.3.6
## [58] UCSC.utils_1.2.0 ScaledMatrix_1.14.0 munsell_0.5.1
## [61] tibble_3.2.1 pillar_1.9.0 htmltools_0.5.8.1
## [64] GenomeInfoDbData_1.2.13 R6_2.5.1 evaluate_1.0.1
## [67] lattice_0.22-6 highr_0.11 bslib_0.8.0
## [70] Rcpp_1.0.13 gridExtra_2.3 SparseArray_1.6.0
## [73] xfun_0.48 buildtools_1.0.0 pkgconfig_2.0.3