slingParams {slingshot} | R Documentation

## 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)

[Package slingshot version 2.2.1 Index]