slingshot (version 2.1.1)

plot3d-SlingshotDataSet: Plot Slingshot output in 3D

Description

Tools for visualizing lineages inferred by slingshot.

Usage

plot3d.SlingshotDataSet(
  x,
  type = NULL,
  linInd = NULL,
  add = FALSE,
  dims = seq_len(3),
  aspect = "iso",
  size = 10,
  col = 1,
  ...
)

Arguments

x

a SlingshotDataSet with results to be plotted.

type

character, the type of output to be plotted, can be one of "lineages", curves, or both (by partial matching), see Details for more.

linInd

integer, an index indicating which lineages should be plotted (default is to plot all lineages). If col is a vector, it will be subsetted by linInd.

add

logical, indicates whether the output should be added to an existing plot.

dims

numeric, which dimensions to plot (default is 1:3).

aspect

either a logical indicating whether to adjust the aspect ratio or a new ratio, see plot3d.

size

numeric, size of points for MST (default is 10), see plot3d.

col

character or numeric, color(s) for lines, see par.

...

additional parameters to be passed to lines3d.

Value

returns NULL.

Details

If type == 'lineages', straight line connectors between cluster centers will be plotted. If type == 'curves', simultaneous principal curves will be plotted.

When type is not specified, the function will first check the curves slot and plot the curves, if present. Otherwise, lineages will be plotted, if present.

Examples

# NOT RUN {
library(rgl)
data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
rd <- cbind(rd, rnorm(nrow(rd)))
pto <- slingshot(rd, cl, start.clus = "1")
sds <- SlingshotDataSet(pto)
plot3d.SlingshotDataSet(sds, type = 'b')

# add to existing plot
plot3d(rd, col = 'grey50', aspect = 'iso')
plot3d.SlingshotDataSet(sds, lwd = 3, add = TRUE)
# }