slingMST: Extract Slingshot minimum spanning tree

In kstreet13/slingshot: Tools for ordering single-cell sequencing

Extract Slingshot minimum spanning tree

Description

Extract the minimum spanning tree from an object containing slingshot output.

Usage

slingMST(x, ...)

## S4 method for signature 'PseudotimeOrdering'
slingMST(x, as.df = FALSE)

## S4 method for signature 'SingleCellExperiment'
slingMST(x, ...)

## S4 method for signature 'SlingshotDataSet'
slingMST(x, as.df = FALSE)

Arguments

x	an object containing slingshot output.
...	additional parameters to be passed to object-specific methods.
as.df	logical, whether to format the output as a data.frame, suitable for plotting with ggplot.

Value

In most cases, output is an igraph object representing the MST. If x is a SlingshotDataSet, then output is an adjacency matrix representing the MST.

Examples

data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
pto <- slingshot(rd, cl, start.clus = '1')
slingMST(pto)

kstreet13/slingshot documentation built on April 6, 2023, 11:12 p.m.