plotPoset {OncoSimulR} | R Documentation

## Plot a poset.

### Description

Plot a poset. Optionally add a root and change names of nodes.

### Usage

    plotPoset(x, names = NULL, addroot = FALSE, box = FALSE, ...)

### Arguments

`x` | A poset. A matrix with two columns where, in each row, the first column is the ancestor and the second the descendant. Note that there might be multiple rows with the same ancestor, and multiple rows with the same descendant. See `poset`.
`names` | If not NULL, a vector of names for the nodes, with the same length as the total number of nodes in a poset (which need not be the same as the number of rows; see `poset`). If `addroot = TRUE`, then 1 + the number of nodes in the poset.
`addroot` | Add a "Root" node to the graph?
`box` | Should the graph be placed inside a box?
`...` | Additional arguments to `plot` (actually, `plot.graphNEL` in the `Rgraphviz` package

).

### Details

The poset is converted to a `graphNEL` object.

### Value

A plot is produced.

### Author(s)

Ramon Diaz-Uriarte

### See Also

`examplePosets`, `poset`

### Examples

    data(examplePosets)
    plotPoset(examplePosets[["p1101"]])

    ## If you will be using that poset a lot, maybe simpler if

    poset701 <- examplePosets[["p701"]]
    plotPoset(poset701, addroot = TRUE)

    ## Compare to Pancreatic cancer figure in Gerstung et al., 2011

    plotPoset(poset701,
              names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
                         "MLL3","PXDN", "TGFBR2"))

    ## If you want to show Root explicitly do

    plotPoset(poset701, addroot = TRUE,
              names = c("Root", "KRAS", "SMAD4", "CDNK2A", "TP53",
                         "MLL3","PXDN", "TGFBR2"))

    ## Of course, names are in the order of nodes, so KRAS is for node 1,
    ##   etc, but the order of entries in the poset does not matter:

    poset701b <- poset701[nrow(poset701):1, ]

    plotPoset(poset701b,
              names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
                         "MLL3","PXDN", "TGFBR2"))

[Package OncoSimulR version 3.2.0 Index]