DPT-class {destiny} | R Documentation

## Diffusion Pseudo Time

### Description

Create pseudotime ordering and assigns cell to one of three branches

### Usage

    DPT(dm, tips = random_root(dm), ..., w_width = 0.1)

### Arguments

`dm` | A `DiffusionMap` object. Its transition probabilities will be used to calculate the DPT
`tips` | The cell index/indices from which to calculate the DPT(s) (integer of length 1-3)
`...` | Unused. All parameters to the right of the `...` have to be specified by name (e.g. `DPT(dm, w_width = 0.2)`)
`w_width` | Window width to use for deciding the branch cutoff

### Details

Treat it as a matrix of pseudotime by subsetting (`[ dim nrow ncol` `as.matrix`), and as a list of pseudodime, and expression vectors (`$ [[ names` `as.data.frame`).

### Value

A `DPT` object:

### Slots

`branch`

  `matrix` (of `integer`) recursive branch labels for each cell (row); `NA` for undeceided. Use `branch_divide` to modify this.

`tips`

  `matrix` (of `logical`) indicating if a cell (row) is a tip of the corresponding banch level (col)

`dm`

  `DiffusionMap` used to create this DPT object

### Examples

    data(guo_norm)
    dm <- DiffusionMap(guo_norm)
    dpt <- DPT(dm)
    str(dpt)

[Package destiny version 3.6.0 Index]