getClusterLineages: Get lineages from cluster centers

In lingxuez/SOUP: Semi-soft Clustering of Single Cell Data

Description

Given cluster centers, construct a linearge using minimum spanning tree (MST) with Euclidean distances. It is often suggested to use a low-dimensional space for identifying MST. A starting or ending cluster can be specified if prior knowledge is available. This code is adapted from the 'getLineages' method in the R package 'slingshot'.

Usage

getClusterLineages(centers, end.clust = NULL, start.clust = NULL,
  dist.fun = NULL)

Arguments

centers	K-by-p' matrix of cluster centers, where p' is usually for the low-dimensional space.
end.clust	(optional) the end point
start.clust	(optional) the starting point

References

Street K, Risso D, Fletcher RB, et al. (2017). "Slingshot: Cell lineage and pseudotime inference for single-cell transcriptomics." bioRxiv. 10.1101/128843

lingxuez/SOUP documentation built on May 28, 2019, 3:38 p.m.