plot.DPT: Plot DPT

In destiny: Creates diffusion maps

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')

destiny documentation built on Nov. 8, 2020, 7:38 p.m.