pairs-SlingshotDataSet: Pairs plot of Slingshot output

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

Pairs plot of Slingshot output

Description

A tool for quickly visualizing lineages inferred by slingshot.

Usage

## S3 method for class '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.

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")
pairs(SlingshotDataSet(pto))

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