FindClusters: Cluster Determination

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization based clustering algorithm. First calculate k-nearest neighbors and construct the SNN graph. Then optimize the modularity function to determine clusters. For a full description of the algorithms, see Waltman and van Eck (2013) The European Physical Journal B.

Usage

FindClusters(object, genes.use = NULL, pc.use = NULL, k.param = 30,
  k.scale = 25, plot.SNN = FALSE, prune.SNN = 1/15, save.SNN = FALSE,
  reuse.SNN = FALSE, do.sparse = FALSE, modularity.fxn = 1,
  resolution = 0.8, algorithm = 1, n.start = 100, n.iter = 10,
  random.seed = 0, print.output = TRUE, temp.file.location = NULL)

Arguments

object	Seurat object
genes.use	Gene expression data
pc.use	Which PCs to use for construction of the SNN graph
k.param	Defines k for the k-nearest neighbor algorithm
k.scale	granularity option for k.param
plot.SNN	Plot the SNN graph
prune.SNN	Stringency of pruning for the SNN graph (0 - no pruning, 1 - prune everything)
save.SNN	Whether to save the SNN in an object slot
reuse.SNN	Force utilization of stored SNN. If none store, this will throw an error.
do.sparse	Option to store and use SNN matrix as a sparse matrix. May be necessary datasets containing a large number of cells.
modularity.fxn	Modularity function (1 = standard; 2 = alternative).
resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
algorithm	Algorithm for modularity optimization (1 = original Louvain algorithm; 2 = Louvain algorithm with multilevel refinement; 3 = SLM algorithm).
n.start	Number of random starts.
n.iter	Maximal number of iterations per random start.
random.seed	Seed of the random number generator.
print.output	Whether or not to print output to the console
temp.file.location	Directory where intermediate files will be written. Specify the ABSOLUTE path.

Value

Returns a Seurat object and optionally the SNN matrix, object@ident has been updated with new cluster info

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.