pairs-SlingshotDataSet {slingshot} | R Documentation

## 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
    sds <- slingshot(rd, cl, start.clus = "1")
    pairs(sds, type = 'curves')

[Package slingshot version 1.5.1 Index]