SlingshotDataSet-class: Class 'SlingshotDataSet'

Description Usage Arguments Details Value Methods (by generic) Slots

Description

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. All slingshot methods can take an object of the class SlingshotDataSet as input and will output the same.

Usage

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

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

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

## S4 method for signature 'SlingshotDataSet,ANY,ANY,ANY'
x[i, j]

Arguments

object

a SlingshotDataSet object.

x

a SlingshotDataSet object.

i

indices to be applied to rows (cells) of the reduced dimensional matrix and cluster labels.

j

indices to be applied to the columns (dimensions) of the reduced dimensional matrix.

Details

Warning: this will remove any existing lineages or curves from the SlingshotDataSet object.

Value

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

Methods (by generic)

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.cluscharacter. The label of the root cluster.

  • end.cluscharacter. Vector of cluster labels indicating the terminal clusters.

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

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

  • distmatrix. A numeric matrix of pairwise cluster distances.

They may also specify how simultaneous principal curves were constructed:

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

  • extendcharacter. 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.

  • reweightlogical. 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.

  • reassignlogical. 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.methodcharacter. 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.

  • Other parameters specified by principal_curve.


slingshot documentation built on Nov. 8, 2020, 5:51 p.m.