GSVA on single-cell RNA-seq data
30 October 2025
Abstract
Here we illustrate how to use GSVA with single-cell RNA sequencing (scRNA-seq) data.
Package
GSVA 2.4.0
License: Artistic-2.0
1 Introduction
GSVA provides now specific support for single-cell data in the algorithm
that runs through the gsvaParam() parameter constructor, and originally
described in the publication by (???). At the moment, this
specific support consists of the following features:
- The input expression data can be stored in different types of data
containers prepared to store sparse single-cell data. These types of
sparse data containers can be broadly categorized in those that only
store the expression values, and those that may store additional row
and column metadata. The currently available value-only containers for
input are
dgCMatrix,SVT_SparseArray, andDelayedMatrix. The currently available container for single-cell data that allows one to input additional row and column metadata is aSingleCellExperimentobject. - While the input single-cell data is always sparse, the output of enrichment
scores will be always dense, and therefore, the container storing those
scores will be different from the input data, typically a
matrixor a denseDelayedMatrixobject. The latter will be particularly used when the total number of values exceeds 2^31, which is the largest 32-bit standard integer value in R. - By default, when the input expression data is stored in a sparse data
container, as it typically happens with single-cell data, then a slightly
a slightly modified GSVA algorithm will run, if GSVA is the choice of
algorithm, by which nonzero values are treated differently from zero values,
leading to slightly different results than those obtained by applying the
classical GSVA algorithm. If we set the parameter
sparse=FALSEin the call togsvaParam(), the classical GSVA algorithm will be used, which for a typical single-cell data set will result in longer running times and larger memory consumption than running it in the default sparse regime for this type of data.
In what follows, we will illustrate the use of GSVA on a publicly available single-cell transcriptomics data set of peripheral blood mononuclear cells (PBMCs) published by Zheng et al. (2017).
2 Import data
We import the PBMC data using the TENxPBMCData package, as a
SingleCellExperiment object, defined in the
SingleCellExperiment package.
library(SingleCellExperiment)
library(TENxPBMCData)
sce <- TENxPBMCData(dataset="pbmc4k")
sce
class: SingleCellExperiment
dim: 33694 4340
metadata(0):
assays(1): counts
rownames(33694): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
ENSG00000268674
rowData names(3): ENSEMBL_ID Symbol_TENx Symbol
colnames: NULL
colData names(11): Sample Barcode ... Individual Date_published
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):3 Quality assessment and pre-processing
Here, we perform a quality assessment and pre-processing steps using the package scuttle (McCarthy et al. 2017). We start identifying mitochondrial genes.
library(scuttle)
is_mito <- grepl("^MT-", rowData(sce)$Symbol_TENx)
table(is_mito)
is_mito
FALSE TRUE
33681 13 Calculate quality control (QC) metrics and filter out low-quality cells.
sce <- quickPerCellQC(sce, subsets=list(Mito=is_mito),
sub.fields="subsets_Mito_percent")
dim(sce)
[1] 33694 4147Figure 1 below shows the empirical cumulative distribution of counts per gene in logarithmic scale.
cntxgene <- rowSums(assays(sce)$counts)+1
plot.ecdf(cntxgene, xaxt="n", panel.first=grid(), xlab="UMI counts per gene",
log="x", main="", xlim=c(1, 1e5), las=1)
axis(1, at=10^(0:5), labels=10^(0:5))
abline(v=100, lwd=2, col="red")
Figure 1: Empirical cumulative distribution of UMI counts per gene
The red vertical bar indicates a cutoff value of 100 UMI counts per gene across all cells, below which genes will be filtered out.
We filter out lowly-expressed genes, by selecting those with at least 100 UMI counts across all cells for downstream analysis.
sce <- sce[cntxgene >= 100, ]
dim(sce)
[1] 8823 4147Calculate library size factors and normalized units of expression in logarithmic scale.
sce <- computeLibraryFactors(sce)
sce <- logNormCounts(sce)
assayNames(sce)
[1] "counts" "logcounts"4 Annotate cell types using GSVA
Here, we illustrate how to annotate cell types in the PBMC data using GSVA.
4.1 Read gene sets in GMT format
First, we fetch a collection of 22 leukocyte gene set signatures, containing
a total 547 genes, which should help to distinguish among 22 mature human
hematopoietic cell type populations isolated from peripheral blood or
in vitro culture conditions, including seven T cell types: naïve and memory B
cells, plasma cells, NK cell, and myeloid subsets. These gene sets have been
used in the benchmarking publication by Diaz-Mejia et al. (2019), and were
originally compiled by the CIBERSORT
developers, where they called it the LM22 signature (Newman et al. 2015). The
LM22 signature is stored in the GSVAdata experiment data
package as a compressed text file in
GMT format, which can
be read into R using the readGMT() function from the GSVA
package, and will return the gene sets into a GeneSetCollection object,
defined in the GSEABase package.
library(GSEABase)
library(GSVA)
fname <- file.path(system.file("extdata", package="GSVAdata"),
"pbmc_cell_type_gene_set_signatures.gmt.gz")
gsets <- readGMT(fname)
gsets
GeneSetCollection
names: B_CELLS_MEMORY, B_CELLS_NAIVE, ..., T_CELLS_REGULATORY_TREGS (22 total)
unique identifiers: AIM2, BANK1, ..., SKAP1 (248 total)
types in collection:
geneIdType: SymbolIdentifier (1 total)
collectionType: NullCollection (1 total)4.2 Add gene identifier type metadata
Note that while gene identifers in the sce object correspond to
Ensembl stable identifiers
(ENSG...), the gene identifiers in the gene sets are
HGNC gene symbols. This, in principle, precludes
matching directly what gene in the single-cell data object sce corresponds to
what gene set in the GeneSetCollection object gsets. However, the
GSVA package can do that matching as long as the appropriate
metadata is present in both objects.
In the case of a GeneSetCollection object, its geneIdType metadata slot
stores the type of gene identifier. In the case of a SingleCellExperiment
object, such as the previous sce object, such metadata is not present.
However, using the function gsvaAnnotation() from the GSVA
package, and the helper function ENSEMBLIdentifier() from the
GSEABase package, we add such metadata to the sce object as
follows.
gsvaAnnotation(sce) <- ENSEMBLIdentifier("org.Hs.eg.db")
gsvaAnnotation(sce)
geneIdType: ENSEMBL (org.Hs.eg.db)4.3 Build parameter object
We first build a parameter object using the function gsvaParam(). By
default, the expression values in the logocounts assay will be selected for
downstream analysis.
gsvapar <- gsvaParam(sce, gsets)
gsvapar
A GSVA::gsvaParam object
expression data:
class: SingleCellExperiment
dim: 8823 4147
metadata(1): annotation
assays(2): counts logcounts
rownames(8823): ENSG00000279457 ENSG00000228463 ... ENSG00000198727
ENSG00000273748
rowData names(3): ENSEMBL_ID Symbol_TENx Symbol
colnames: NULL
colData names(22): Sample Barcode ... discard sizeFactor
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
using assay: logcounts
using annotation:
geneIdType: ENSEMBL (org.Hs.eg.db)
gene sets:
GeneSetCollection
names: B_CELLS_MEMORY, B_CELLS_NAIVE, ..., T_CELLS_REGULATORY_TREGS (22 total)
unique identifiers: AIM2, BANK1, ..., SKAP1 (248 total)
types in collection:
geneIdType: SymbolIdentifier (1 total)
collectionType: NullCollection (1 total)
gene set size: [1, Inf]
kcdf: auto
kcdfNoneMinSampleSize: 200
tau: 1
maxDiff: TRUE
absRanking: FALSE
sparse: TRUE
checkNA: auto
missing data: didn't check
ondisk: no
nonzero values: less than 2^31 (INT_MAX)4.4 Calculate GSVA scores
While at this point, we could already run the entire GSVA algorithm with a call
to the gsva(gsvapar) function. We show here how to do it in two steps.
First we calculate GSVA rank values using the function gsvaRanks().
gsvaranks <- gsvaRanks(gsvapar)
gsvaranks
A GSVA::gsvaRanksParam object
expression data:
class: SingleCellExperiment
dim: 8823 4147
metadata(1): annotation
assays(3): counts logcounts gsvaranks
rownames(8823): ENSG00000279457 ENSG00000228463 ... ENSG00000198727
ENSG00000273748
rowData names(3): ENSEMBL_ID Symbol_TENx Symbol
colnames: NULL
colData names(22): Sample Barcode ... discard sizeFactor
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
using assay: gsvaranks
using annotation:
geneIdType: ENSEMBL (org.Hs.eg.db)
gene sets:
GeneSetCollection
names: B_CELLS_MEMORY, B_CELLS_NAIVE, ..., T_CELLS_REGULATORY_TREGS (22 total)
unique identifiers: AIM2, BANK1, ..., SKAP1 (248 total)
types in collection:
geneIdType: SymbolIdentifier (1 total)
collectionType: NullCollection (1 total)
gene set size: [1, Inf]
kcdf: auto
kcdfNoneMinSampleSize: 200
tau: 1
maxDiff: TRUE
absRanking: FALSE
sparse: TRUE
checkNA: auto
missing data: didn't check
ondisk: no
nonzero values: less than 2^31 (INT_MAX)Second, we calculate the GSVA scores using the output of gsvaRanks() as input
to the function gsvaScores(). By default, this function will calculate the
scores for all gene sets specified in the input parameter object.
es <- gsvaScores(gsvaranks)
es
class: SingleCellExperiment
dim: 22 4147
metadata(0):
assays(1): es
rownames(22): B_CELLS_MEMORY B_CELLS_NAIVE ... T_CELLS_GAMMA_DELTA
T_CELLS_REGULATORY_TREGS
rowData names(1): gs
colnames: NULL
colData names(22): Sample Barcode ... discard sizeFactor
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):However, we could calculate the scores for another collection of gene sets by
updating them in the gsvaranks object as follows.
geneSets(gsvaranks) <- geneSets(gsvapar)[1:2]
es2 <- gsvaScores(gsvaranks)4.5 Using GSVA scores to assign cell types
Following Amezquita et al. (2020), and some of the steps described in
“Chapter 5 Clustering” of the first version of the
OSCA book,
we use GSVA scores to build a nearest-neighbor graph of the cells using the
function buildSNNGraph() from the scran
package (Lun, McCarthy, and Marioni 2016). The parameter k in the call to buildSNNGraph()
specifies the number of nearest neighbors to consider during graph
construction, and here we set k=20 because it leads to a number of clusters
close to the expected number of cell types.
library(scran)
g <- buildSNNGraph(es, k=20, assay.type="es")Second, we use the function cluster_walktrap() from the igraph
package (Csardi and Nepusz 2006), to cluster cells by finding densely connected
subgraphs. We store the resulting vector of cluster indicator values into the
sce object using the function colLabels().
library(igraph)
colLabels(es) <- factor(cluster_walktrap(g)$membership)
table(colLabels(es))
1 2 3 4 5 6 7 8
495 601 502 525 972 191 345 516 Similarly to Diaz-Mejia et al. (2019), we apply a simple cell type assignment
algorithm, which consists of selecting at each cell the gene set with highest
GSVA score, tallying the selected gene sets per cluster, and assigning to the
cluster the most frequent gene set, storing that assignment into the sce
object with the function colLabels().
## whmax <- apply(assay(es), 2, which.max)
whmax <- apply(assay(es), 2, function(x) which.max(as.vector(x)))
gsxlab <- split(rownames(es)[whmax], colLabels(es))
gsxlab <- names(sapply(sapply(gsxlab, table), which.max))
colLabels(es) <- factor(gsub("[0-9]\\.", "", gsxlab))[colLabels(es)]
table(colLabels(es))
B_CELLS_NAIVE EOSINOPHILS NK_CELLS_ACTIVATED NK_CELLS_RESTING
601 1027 495 191
T_CELLS_CD4_NAIVE T_CELLS_CD8
1488 345 We can visualize the cell type assignments by projecting cells dissimilarity in two dimensions with a principal components analysis (PCA) on the GSVA scores, and coloring cells using the previously assigned clusters.
library(RColorBrewer)
res <- prcomp(assay(es))
varexp <- res$sdev^2 / sum(res$sdev^2)
nclusters <- nlevels(colLabels(es))
hmcol <- colorRampPalette(brewer.pal(nclusters, "Set1"))(nclusters)
par(mar=c(4, 5, 1, 1))
plot(res$rotation[, 1], res$rotation[, 2], col=hmcol[colLabels(es)], pch=19,
xlab=sprintf("PCA 1 (%.0f%%)", varexp[1]*100),
ylab=sprintf("PCA 2 (%.0f%%)", varexp[2]*100),
las=1, cex.axis=1.2, cex.lab=1.5)
legend("topright", gsub("_", " ", levels(colLabels(es))), fill=hmcol, inset=0.01)
Figure 2: Cell type assignments of PBMC scRNA-seq data, based on GSVA scores
Finally, if we want to better understand why a specific cell type is annotated
to a given cell, we can use the gsvaEnrichment() function, which will show
a GSEA enrichment plot. This function takes as input the output of
gsvaRanks(), a given column (cell) in the input singl-cell data, and a given
gene set. In Figure 3 below, we show such a plot for the
first cell annotated to the eosinophil cell type.
firsteosinophilcell <- which(colLabels(es) == "EOSINOPHILS")[1]
par(mar=c(4, 5, 1, 1))
gsvaEnrichment(gsvaranks, column=firsteosinophilcell, geneSet="EOSINOPHILS",
cex.axis=1.2, cex.lab=1.5, plot="ggplot")
Figure 3: GSVA enrichment plot of the EOSINOPHILS gene set in the expression profile of the first cell annotated to that cell type
In the previous call to gsvaEnrichment() we used the argument plot="ggplot"
to produce a plot with the ggplot2
package. By default, if we call gsvaEnrichment() interactively, it will
produce a plot using “base R”, but either when we do it non-interactively, or
when we set plot="no" it will return a data.frame object with the enrichment
data.
5 Forthcoming features
These are features that we are working on and we expect to have them implemented in the near future (e.g., next release):
The parallelization for single-cell data stored using a
DelayedArraybackend, such as HDF5, is not yet implemented. If you have enough RAM, you can attempt converting the data set to anSVT_SparseArrayin main memory (see subsection 8.2 of the vignette of the SparseArray package for further information).A specific implementation of the other methods ssGSEA, PLAGE and zscore to work on large datasets stored using a
DelayedArraybackend, such as HDF5, is not yet available.
We are still benchmarking and testing this version of GSVA for single-cell data. If you encounter problems or have suggestions, do not hesitate to contact us by opening an issue in the GSVA GitHub repo.
Session information
Here is the output of sessionInfo() on the system on which this document was
compiled running pandoc 2.7.3:
sessionInfo()
R version 4.5.1 Patched (2025-08-23 r88802)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
locale:
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[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] igraph_2.2.1 scran_1.38.0
[3] scuttle_1.20.0 TENxPBMCData_1.27.0
[5] HDF5Array_1.38.0 h5mread_1.2.0
[7] rhdf5_2.54.0 DelayedArray_0.36.0
[9] SparseArray_1.10.0 S4Arrays_1.10.0
[11] abind_1.4-8 Matrix_1.7-4
[13] SingleCellExperiment_1.32.0 sva_3.58.0
[15] BiocParallel_1.44.0 genefilter_1.92.0
[17] mgcv_1.9-3 nlme_3.1-168
[19] RColorBrewer_1.1-3 edgeR_4.8.0
[21] limma_3.66.0 GSVAdata_1.45.0
[23] SummarizedExperiment_1.40.0 GenomicRanges_1.62.0
[25] Seqinfo_1.0.0 MatrixGenerics_1.22.0
[27] matrixStats_1.5.0 hgu95a.db_3.13.0
[29] GSEABase_1.72.0 graph_1.88.0
[31] annotate_1.88.0 XML_3.99-0.19
[33] org.Hs.eg.db_3.22.0 AnnotationDbi_1.72.0
[35] IRanges_2.44.0 S4Vectors_0.48.0
[37] Biobase_2.70.0 BiocGenerics_0.56.0
[39] generics_0.1.4 GSVA_2.4.0
[41] BiocStyle_2.38.0
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[85] statmod_1.5.1 bit64_4.6.0-1 References
Amezquita, Robert A, Aaron TL Lun, Etienne Becht, Vince J Carey, Lindsay N Carpp, Ludwig Geistlinger, Federico Marini, et al. 2020. “Orchestrating Single-Cell Analysis with Bioconductor.” Nature Methods 17 (2): 137–45.
Csardi, Gabor, and Tamas Nepusz. 2006. “The Igraph Software Package for Complex Network Research.” InterJournal Complex Systems: 1695. https://igraph.org.
Diaz-Mejia, J Javier, Elaine C Meng, Alexander R Pico, Sonya A MacParland, Troy Ketela, Trevor J Pugh, Gary D Bader, and John H Morris. 2019. “Evaluation of Methods to Assign Cell Type Labels to Cell Clusters from Single-Cell Rna-Sequencing Data.” F1000Research 8: ISCB–Comm.
Lun, Aaron TL, Davis J McCarthy, and John C Marioni. 2016. “A Step-by-Step Workflow for Low-Level Analysis of Single-Cell Rna-Seq Data with Bioconductor.” F1000Research 5: 2122.
McCarthy, Davis J, Kieran R Campbell, Aaron TL Lun, and Quin F Wills. 2017. “Scater: Pre-Processing, Quality Control, Normalization and Visualization of Single-Cell Rna-Seq Data in R.” Bioinformatics 33 (8): 1179–86.
Newman, Aaron M, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, and Ash A Alizadeh. 2015. “Robust Enumeration of Cell Subsets from Tissue Expression Profiles.” Nature Methods 12 (5): 453–57.
Zheng, Grace XY, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, et al. 2017. “Massively Parallel Digital Transcriptional Profiling of Single Cells.” Nature Communications 8 (1): 14049.