slingParams: Methods for parameters used by Slingshot

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

Methods for parameters used by Slingshot

Description

Extracts additional control parameters used by Slingshot in lineage inference and fitting simultaneous principal curves.

Usage

slingParams(x)

## S4 method for signature 'PseudotimeOrdering'
slingParams(x)

## S4 method for signature 'SingleCellExperiment'
slingParams(x)

## S4 method for signature 'SlingshotDataSet'
slingParams(x)

Arguments

x	an object containing slingshot output.

Value

The list of additional parameters used by Slingshot. These include parameters related to the cluster-based minimum spanning tree:

• start.clus character. The label of the root cluster, or a vector of cluster labels giving the root clusters of each disjoint component of the graph.

• end.clus character. Vector of cluster labels indicating terminal clusters.

• start.given logical. A logical value indicating whether the initial state was pre-specified.

• end.given logical. A vector of logical values indicating whether each terminal state was pre-specified

• omega numeric or logical. Granularity parameter determining the maximum edge length for building the MST. See getLineages.

• omega_scale numeric. Scaling factor used for setting maximum edge length when omega = TRUE. See getLineages.

They may also specify how simultaneous principal curves were constructed (for a complete listing, see getCurves:

• shrink logical or numeric between 0 and 1. Determines whether and how much to shrink branching lineages toward their shared average curve.

• extend character. Specifies the method for handling root and leaf clusters of lineages when constructing the initial, piece-wise linear curve. Accepted values are 'y' (default), 'n', and 'pc1'. See getCurves for details.

• reweight logical. Indicates whether to allow cells shared between lineages to be reweighted during curve-fitting. If TRUE, cells shared between lineages will be iteratively reweighted based on the quantiles of their projection distances to each curve.

• reassign logical. Indicates whether to reassign cells to lineages at each iteration. If TRUE, cells will be added to a lineage when their projection distance to the curve is less than the median distance for all cells currently assigned to the lineage. Additionally, shared cells will be removed from a lineage if their projection distance to the curve is above the 90th percentile and their weight along the curve is less than 0.1.

• shrink.method character. Denotes how to determine the amount of shrinkage for a branching lineage. Accepted values are the same as for kernel in the density function (default is "cosine"), as well as "tricube" and "density". See getCurves for details.

• approx_points numeric. Number of points to use in estimating curves. See getCurves for details.

• allow.breaks logical. Whether to allow curves that diverge very early on in a trajectory to have different starting points.

• Other parameters specified by principal_curve.

Examples

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

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