quickCluster: Quick clustering of cells

In MarioniLab/scran: Methods for Single-Cell RNA-Seq Data Analysis

Quick clustering of cells

Description

Cluster similar cells based on their expression profiles, using either log-expression values or ranks.

Usage

quickCluster(x, ...)

## S4 method for signature 'ANY'
quickCluster(
  x,
  min.size = 100,
  method = c("igraph", "hclust"),
  use.ranks = FALSE,
  d = NULL,
  subset.row = NULL,
  min.mean = NULL,
  graph.fun = "walktrap",
  BSPARAM = bsparam(),
  BPPARAM = SerialParam(),
  block = NULL,
  block.BPPARAM = SerialParam(),
  ...
)

## S4 method for signature 'SummarizedExperiment'
quickCluster(x, ..., assay.type = "counts")

Arguments

x	A numeric count matrix where rows are genes and columns are cells. Alternatively, a SummarizedExperiment object containing such a matrix.
...	For the generic, further arguments to pass to specific methods. For the ANY method, additional arguments to be passed to NNGraphParam for method="igraph", or to be included in cut.params argument for HclustParam when method="hclust". For the SummarizedExperiment method, additional arguments to pass to the ANY method.
min.size	An integer scalar specifying the minimum size of each cluster.
method	String specifying the clustering method to use. "hclust" uses hierarchical clustering while "igraph" uses graph-based clustering.
use.ranks	A logical scalar indicating whether clustering should be performed on the rank matrix, i.e., based on Spearman's rank correlation.
d	An integer scalar specifying the number of principal components to retain. If d=NULL and use.ranks=TRUE, this defaults to 50. If d=NULL and use.rank=FALSE, the number of PCs is chosen by denoisePCA. If d=NA, no dimensionality reduction is performed and the gene expression values (or their rank equivalents) are directly used in clustering.
subset.row	See ?"scran-gene-selection".
min.mean	A numeric scalar specifying the filter to be applied on the average count for each filter prior to computing ranks. Only used when use.ranks=TRUE, see ?scaledColRanks for details.
graph.fun	A function specifying the community detection algorithm to use on the nearest neighbor graph when method="igraph". Usually obtained from the igraph package.
BSPARAM	A BiocSingularParam object specifying the algorithm to use for PCA, if d is not NA.
BPPARAM	A BiocParallelParam object to use for parallel processing within each block.
block	A factor of length equal to ncol(x) specifying whether clustering should be performed within pre-specified blocks. By default, all columns in x are treated as a single block.
block.BPPARAM	A BiocParallelParam object specifying whether and how parallelization should be performed across blocks, if block is non-NULL and has more than one level.
assay.type	A string specifying which assay values to use.

Details

This function provides a convenient wrapper to quickly define clusters of a minimum size min.size. Its intended use is to generate “quick and dirty” clusters for use in computeSumFactors. Two clustering strategies are available:

• If method="hclust", a distance matrix is constructed; hierarchical clustering is performed using Ward's criterion; and cutreeDynamic is used to define clusters of cells.

• If method="igraph", a shared nearest neighbor graph is constructed using the buildSNNGraph function. This is used to define clusters based on highly connected communities in the graph, using the graph.fun function.

By default, quickCluster will apply these clustering algorithms on the principal component (PC) scores generated from the log-expression values. These are obtained by running denoisePCA on HVGs detected using the trend fitted to endogenous genes with modelGeneVar. If d is specified, the PCA is directly performed on the entire x and the specified number of PCs is retained.

It is also possible to use the clusters from this function for actual biological interpretation. In such cases, users should set min.size=0 to avoid aggregation of small clusters. However, it is often better to call the relevant functions (modelGeneVar, denoisePCA and buildSNNGraph) manually as this provides more opportunities for diagnostics when the meaning of the clusters is important.

Value

A character vector of cluster identities for each cell in x.

Clustering within blocks

We can break up the dataset by specifying block to cluster cells, usually within each batch or run. This generates clusters within each level of block, which is entirely adequate for applications like computeSumFactors where the aim of clustering is to separate dissimilar cells rather than group together all similar cells. Blocking reduces computational work considerably by allowing each level to be processed independently, without compromising performance provided that there are enough cells within each batch.

Indeed, for applications like computeSumFactors, we can use block even in the absence of any known batch structure. Specifically, we can set it to an arbitrary factor such as block=cut(seq_len(ncol(x)), 10) to split the cells into ten batches of roughly equal size. This aims to improve speed, especially when combined with block.PARAM to parallelize processing of the independent levels.

Using ranks

If use.ranks=TRUE, clustering is instead performed on PC scores obtained from scaled and centred ranks generated by scaledColRanks. This effectively means that clustering uses distances based on the Spearman's rank correlation between two cells. In addition, if x is a dgCMatrix and BSPARAM has deferred=TRUE, ranks will be computed without loss of sparsity to improve speed and memory efficiency during PCA.

When use.ranks=TRUE, the function will filter out genes with average counts (as defined by calculateAverage) below min.mean prior to computing ranks. This removes low-abundance genes with many tied ranks, especially due to zeros, which may reduce the precision of the clustering. We suggest setting min.mean to 1 for read count data and 0.1 for UMI data - the function will automatically try to determine this from the data if min.mean=NULL.

Setting use.ranks=TRUE is invariant to scaling normalization and avoids circularity between normalization and clustering, e.g., in computeSumFactors. However, the default is to use the log-expression values with use.ranks=FALSE, as this yields finer and more precise clusters.

Enforcing cluster sizes

With method="hclust", cutreeDynamic is used to ensure that all clusters contain a minimum number of cells. However, some cells may not be assigned to any cluster and are assigned identities of "0" in the output vector. In most cases, this is because those cells belong in a separate cluster with fewer than min.size cells. The function will not be able to call this as a cluster as the minimum threshold on the number of cells has not been passed. Users are advised to check that the unassigned cells do indeed form their own cluster. Otherwise, it may be necessary to use a different clustering algorithm.

When using method="igraph", clusters are first identified using the specified graph.fun. If the smallest cluster contains fewer cells than min.size, it is merged with the closest neighbouring cluster. In particular, the function will attempt to merge the smallest cluster with each other cluster. The merge that maximizes the modularity score is selected, and a new merged cluster is formed. This process is repeated until all (merged) clusters are larger than min.size.

Author(s)

Aaron Lun and Karsten Bach

References

van Dongen S and Enright AJ (2012). Metric distances derived from cosine similarity and Pearson and Spearman correlations. arXiv 1208.3145

Lun ATL, Bach K and Marioni JC (2016). Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17:75

See Also

computeSumFactors, where the clustering results can be used as clusters=.

buildSNNGraph, for additional arguments to customize the clustering when method="igraph".

cutreeDynamic, for additional arguments to customize the clustering when method="hclust".

scaledColRanks, to get the rank matrix that was used with use.rank=TRUE.

quickSubCluster, for a related function that uses a similar approach for subclustering.

Examples

library(scuttle)
sce <- mockSCE()

# Basic application (lowering min.size for this small demo):
clusters <- quickCluster(sce, min.size=50)
table(clusters)

# Operating on ranked expression values:
clusters2 <- quickCluster(sce, min.size=50, use.ranks=TRUE)
table(clusters2)

# Using hierarchical clustering:
clusters <- quickCluster(sce, min.size=50, method="hclust")
table(clusters)

MarioniLab/scran documentation built on Sept. 7, 2024, 6:25 a.m.