slingMST {slingshot} | R Documentation

## 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)

[Package slingshot version 2.0.0 Index]