SlingshotDataSet-class {slingshot} | R Documentation

## Class `SlingshotDataSet`

### Description

This was the original class for storing `slingshot` results, but we now generally reommend using the `PseudotimeOrdering` class, instead. Most `slingshot` functions will still work with `SlingshotDataSet` objects, but will return `PseudotimeOrdering` objects, by default. To update old `SlingshotDataSet` objects, we have provided the `as.PseudotimeOrdering` conversion function. The only functions that require `SlingshotDataSet` objects are the plotting functions.

The `SlingshotDataSet` class holds data relevant for performing lineage inference with the `slingshot` package, primarily a reduced dimensional representation of the data and a set of cluster labels.

### Usage

    ## S4 method for signature 'SlingshotDataSet'
    show(object)

    ## S4 method for signature 'SlingshotDataSet,ANY'
    reducedDim(x)

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

### Arguments

`object` | a `SlingshotDataSet` object.
`x` | a `SlingshotDataSet` object.

### Value

The accessor functions `reducedDim`, `clusterLabels`, `lineages`, `adjacency`, `curves`, and `slingParams` return the corresponding elements of a `SlingshotDataSet`. The functions `slingPseudotime` and `slingCurveWeights` extract useful output elements of a `SlingshotDataSet`, provided that curves have already been fit with either `slingshot` or `getCurves`.

### Methods (by generic)

- `show`: a short summary of a `SlingshotDataSet` object.

- `reducedDim`: returns the matrix representing the reduced dimensional dataset.

### Slots

`reducedDim`

  matrix. An `n` by `p` numeric matrix or data frame giving the coordinates of the cells in a reduced dimensionality space.

`clusterLabels`

  matrix or character. An `n` by `K` matrix of weights indicating each cell's cluster assignment or a character vector of cluster assignments, which will be converted into a binary matrix.

`lineages`

  list. A list with each element a character vector of cluster names representing a lineage as an ordered set of clusters.

`adjacency`

  matrix. A binary matrix describing the adjacency between clusters induced by the minimum spanning tree.

`curves`

  list. A list of `principal_curve` objects produced by `getCurves`.

`slingParams`

  list. Additional parameters used by Slingshot. These may specify how the minimum spanning tree on clusters was constructed:

  - `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`.

### See Also

`PseudotimeOrdering`

[Package slingshot version 2.0.0 Index]