plot-SlingshotDataSet: Plot Slingshot output

In kstreet13/slingshot: Tools for ordering single-cell sequencing

Plot Slingshot output

Description

Tools for visualizing lineages inferred by slingshot.

Usage

## S3 method for class 'SlingshotDataSet'
plot(
  x,
  type = NULL,
  linInd = NULL,
  show.constraints = FALSE,
  add = FALSE,
  dims = seq_len(2),
  asp = 1,
  cex = 2,
  lwd = 2,
  col = 1,
  ...
)

## S3 method for class 'SlingshotDataSet'
lines(x, type = NULL, dims = seq_len(2), ...)

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.
show.constraints	logical, whether or not the user-specified initial and terminal clusters should be specially denoted by green and red dots, respectively.
add	logical, indicates whether the output should be added to an existing plot.
dims	numeric, which dimensions to plot (default is 1:2).
asp	numeric, the y/x aspect ratio, see plot.window.
cex	numeric, amount by which points should be magnified, see par.
lwd	numeric, the line width, see par.
col	character or numeric, color(s) for lines, see par.
...	additional parameters to be passed to lines.

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.

Value

returns NULL.

Examples

data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
pto <- slingshot(rd, cl, start.clus = "1")
plot(SlingshotDataSet(pto), type = 'b')

# add to existing plot
sds <- as.SlingshotDataSet(pto)
plot(rd, col = 'grey50', asp = 1)
lines(sds, lwd = 3)

kstreet13/slingshot documentation built on April 6, 2023, 11:12 p.m.