slingshot (version 2.1.1)

pairs-SlingshotDataSet: Pairs plot of Slingshot output

Description

A tool for quickly visualizing lineages inferred by slingshot.

Usage

# S3 method for SlingshotDataSet
pairs(
  x,
  type = NULL,
  show.constraints = FALSE,
  col = NULL,
  pch = 16,
  cex = 1,
  lwd = 2,
  ...,
  labels,
  horInd = seq_len(nc),
  verInd = seq_len(nc),
  lower.panel = FALSE,
  upper.panel = TRUE,
  diag.panel = NULL,
  text.panel = textPanel,
  label.pos = 0.5 + has.diag/3,
  line.main = 3,
  cex.labels = NULL,
  font.labels = 1,
  row1attop = TRUE,
  gap = 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.

show.constraints

logical, whether or not the user-specified initial and terminal clusters should be specially denoted by green and red dots, respectively.

col

character, color vector for points.

pch

integer or character specifying the plotting symbol, see par.

cex

numeric, amount by which points should be magnified, see par.

lwd

numeric, the line width, see par.

...

additional parameters for plot or axis, see pairs.

labels

character, the names of the variables, see pairs.

horInd

see pairs.

verInd

see pairs.

lower.panel

see pairs.

upper.panel

see pairs.

diag.panel

see pairs.

text.panel

see pairs.

label.pos

see pairs.

line.main

see pairs.

cex.labels

see pairs.

font.labels

see pairs.

row1attop

see pairs.

gap

see pairs.

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")
pairs(SlingshotDataSet(pto))

# }