TSCANorder: TSCANorder

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

TSCANorder

Description

Construct TSCAN order after exprmclust

Usage

TSCANorder(
  mclustobj,
  startcluster = NULL,
  MSTorder = NULL,
  orderonly = F,
  flip = F,
  listbranch = F,
  divide = T
)

Arguments

mclustobj	The exact output of the exprmclust function.
startcluster	A numeric value specifying the cluster where pseudotime starts from.
MSTorder	A numeric vector specifying the order of clusters.
orderonly	Only return the ordering. State or pseudotime information will not be returned
flip	whether to flip the ordering
listbranch	whether to list the ordering results of all possible branches in MST. Only works if MSTorder in NULL.
divide	for a cluster that are linked to multiple clusters, whether each cell in the cluster can only appear in one of the branches. If TRUE, then the cells in the cluster will be divided based on their distances to the linked clusters and placed separately in different branches. If FALSE, then all cells in the cluster will appear in multiple branches.

Details

This function takes the exact output of exprmclust function and construct TSCAN order by mapping all cells onto the path that connects cluster centers. Users can also specify their own path.

Value

if orderonly = F, a vector of ordered cell names. if orderonly = T, a data frame of ordered cell names, cell states and pseudotime.

Author(s)

Zhicheng Ji, Hongkai Ji <[e-mail]>

Examples

data(lpsdata)
procdata <- preprocess(lpsdata)
lpsmclust <- exprmclust(procdata)
TSCANorder(lpsmclust)

zji90/TSCAN documentation built on Sept. 14, 2022, 10:56 a.m.