cluster.assignment: Partition cells into disjoint clusters

In minzheguo/SINCERA: An R implementation of SINCERA pipeline for processing single-cell RNA-seq data.

Description

Partition cells into disjoint clusters

Usage

cluster.assignment(object, feature.type = "gene", rds.dims = 1:3,
  update.cellgroup = T, clustering.method = "hc", verbose = T, ...)

Arguments

object	A sincera object
feature.type	The feature space used for clustering: "gene" - means gene expression space, "pca" - means reduced dimension space using PCA
rds.dims	A numberic vector specified the reduced dimensions used for clustering. Only take effect when the feature.type is "pca" or "tsne"
update.cellgroup	The clustering result will be saved to the "CLUSTER" meta data. If TRUE, the GROUP meta data will be updated as well.
clustering.method	The cluster identification algorithm, possible values include pam, kmeans, hc, graph, tight, consensus
verbose	If TRUE, print the verbose messages

Details

The default clustering method is hc - hierarchical clustering with Pearson's correlation based distance and average linkage. Possible parameters include: h - if not NULL, cut dendrogram tree at the height h; k - if not NULL, cut dendrogram tree to generate k clusters; if both k and h are not NULL, k will be used; If both k and h are NULL, the algorithm will find the largest k that contains no more than num.singleton singleton clusters; num.singleton - the number of singleton clusters allowed; distance.method - the method to calculate cell distance, possible values include pearson, spearman, euclidean; linkage.method - linkage method, possible values include average, complete, ward.D2; do.shift - if TRUE, shit column mean to 0.

When clustering.method is graph, the function utilizes the graph based method described in Shekhar et al., 2016, which first constructs a kNN graph of cells and then applies a community detection algorithm to partition cells. Possible parameters include: num.nn - The number of nearest neighbors considered during the kNN graph construction; do.jaccard - If TRUE, weigh kNN graph edges using Jaccard similarity; community.method - The community detection method, possible values include louvain, infomap, walktrap, spinglass, edge_betweenness, label_prop, optimal, fast_greedy.

When clustering.method is tight, the function utilizes tightClust::tight.clust() to perform tight clustering. Note that this algorithm may produce a partial partition of cells. Cells will be assigned with "-1" membership if they are not assigned to any found tight clusters. please refer to ?tightClust::tight.clust for more informaiton.

When clustering.method is consensus, the function utilizes ConsensusClusterPlus::ConsensusClusterPlus() to perform consensus clustering; the parameter "min.area.increase" is a threshold value for determining the number of clusters; let k be the current choice of the number of clusters, if the delta area from k-1 to k is greater than min.area.increase, k will be increased by 1 until the delta area increase is below min.area.increase or k=maxK. The calculation of delta area is defined in the original paper of ConsensusClusterPlus (Wilkerson et al., Bioinformatics 2010). Please refer to ?ConsensusClusterPlus::ConsensusClusterPlus for the setting of other parameters.

When clustering.method is kmeans, the function utilizes stats::kmeans() to perform k-means clustering; please refer to ?kmeans for parameters and more informaiton.

When clustering.method is pam, the function utilizes cluster::pam() to perform Partitioning Around Medoids clustering; please refer to ?cluster::pam for parameters and more information.

Value

The update sincera object with clustering results in the "CLUSTER" meta data, use getCellMeata with name="CLUSTER" to assess the result

minzheguo/SINCERA documentation built on Feb. 3, 2021, 2:31 p.m.