slingshot_conditions {condiments} | R Documentation

## Refitting slingshot per condition

### Description

Based on an original slingshot object, refit one trajectory per condition, using the same skeleton.

### Usage

    slingshot_conditions(sds, ...)

    ## S4 method for signature 'SlingshotDataSet'
    slingshot_conditions(
      sds,
      conditions,
      approx_points = 100,
      adjust_skeleton = TRUE,
      ...
    )

    ## S4 method for signature 'SingleCellExperiment'
    slingshot_conditions(
      sds,
      conditions,
      approx_points = 100,
      adjust_skeleton = TRUE,
      ...
    )

    ## S4 method for signature 'PseudotimeOrdering'
    slingshot_conditions(
      sds,
      conditions,
      approx_points = 100,
      adjust_skeleton = TRUE,
      ...
    )

### Arguments

`sds` | A slingshot object already run on the full dataset. Can be either a `SlingshotDataSet` or a `SingleCellExperiment` object.
`...` | Other arguments passed to `getCurves`
`conditions` | Either the vector of conditions, or a character indicating which column of the metadata contains this vector.
`approx_points` | Passed to `getCurves`
`adjust_skeleton` | Boolean, default to 'TRUE'. Whether to recompute the locations of the nodes after fitting per conditions.

### Value

A list of `SlingshotDataSet`, one per condition.

### Examples

    data('slingshotExample', package = "slingshot")
    rd <- slingshotExample$rd
    cl <- slingshotExample$cl
    condition <- factor(rep(c('A','B'), length.out = nrow(rd)))
    condition[110:139] <- 'A'
    sds <- slingshot::slingshot(rd, cl)
    sdss <- slingshot_conditions(sds, condition)

[Package condiments version 1.2.0 Index]