plot.DPT {destiny} | R Documentation

## Plot DPT

### Description

Plots diffusion components from a Diffusion Map and the accompanying Diffusion Pseudo Time (`DPT`)

### Usage

    plot.DPT(x, root = NULL, paths_to = integer(0L), dcs = 1:2,
      divide = integer(0L), w_width = 0.1, col_by = "dpt",
      col_path = rev(palette()), col_tip = "red", ..., col = NULL,
      legend_main = col_by)

    ## S4 method for signature 'DPT,numeric'
    plot(x, y, ...)

    ## S4 method for signature 'DPT,missing'
    plot(x, y, ...)

### Arguments

`x` | A `DPT` object.
`paths_to` | Numeric Branch IDs. Are used as target(s) for the path(s) to draw.
`dcs` | The dimensions to use from the DiffusionMap
`divide` | If `col_by = 'branch'`, this specifies which branches to divide. (see `branch_divide`)
`w_width` | Window width for smoothing the path (see `smth.gaussian`)
`col_by` | Color by 'dpt' (DPT starting at `branches[[1]]`), 'branch', or a veriable of the data.
`col_path` | Colors for the path or a function creating n colors
`col_tip` | Color for branch tips
`...` | Graphical parameters supplied to `plot.DiffusionMap`
`col` | See `plot.DiffusionMap`. This overrides `col_by`
`legend_main` | See `plot.DiffusionMap`.
`y, root` | Root branch ID. Will be used as the start of the DPT. (default: lowest branch ID) (If longer than size 1, will be interpreted as `c(root, branches)`)

### Value

The return value of the underlying call is returned, i.e. a scatterplot3d or rgl object for 3D plots.

### Examples

    data(guo_norm)
    dm <- DiffusionMap(guo_norm)
    dpt <- DPT(dm)
    plot(dpt)
    plot(dpt, 2L,      col_by = 'branch')
    plot(dpt, 1L, 2:3, col_by = 'num_cells')
    plot(dpt, col_by = 'DPT3')

[Package destiny version 3.0.1 Index]