slingshot (version 2.1.1)

plot-SlingshotDataSet: Plot Slingshot output

Description

Tools for visualizing lineages inferred by slingshot.

Usage

# S3 method for 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 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.

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 {
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)

# }