guided_MST: guided_MST
In zji90/TSCAN: TSCAN: Tools for Single-Cell ANalysis

View source: R/guided_MST.R

guided_MST

R Documentation

guided_MST

Description

Minimum spanning tree to guide pseudotime construction

Usage

guided_MST(dr, clu)

Arguments

`dr`	A numeric matrix of reduced dimensions. Can be from PCA, t-sne, UMAP, diffusion map, and many others. Each row is a cell and each column is a reduced dimension. Row names should be the cell names.
`clu`	A named vector of cell clustering. Names are the cell names. Need to correspond to dr.

Details

This function should be used when users have already performed PCA or other dimension reductions, and cell clustering. This function will plot a minimum-spanning-tree that helps users to determine which cell clusters should be linked in what order. The result can be fed into guided_tscan function to get the actual pseudotime.