groot.plot {geneplast} | R Documentation

## Plot the inferred evolutionary root of a given OG or the map of LCAs of a given species.

### Description

Plot the inferred evolutionary root of a given OG onto the species tree or the map of LCAs of a given species.

### Usage

    groot.plot(ogr, whichOG, fname="gproot",  width=4.5, height=6.5, cex.lab=0.3,
      cex.nodes=0.6, adj.tips=c(1, 0.5), lab.offset=1.5, col.tips=c("green2","grey"),
      col.edges=c("black","grey"), col.root="red", plot.sspnames=TRUE,
      plot.subtree=FALSE, plot.lcas=FALSE)

### Arguments

`ogr` | this argument is an object of class 'OGR' evaluated by the groot `groot` method.
`whichOG` | a single character value indicating the OG to be plotted.
`fname` | a character string naming a file.
`width` | a single numeric value specifying the width of the graphics region in inches.
`height` | a single numeric value specifying the height of the graphics region in inches.
`cex.lab` | numeric character expansion factor for tip labels.
`cex.nodes` | numeric expansion factor for node symbols.
`adj.tips` | two numeric values specifying the adjustment of the labels.
`lab.offset` | a single numeric value specifying the offset of the labels.
`col.tips` | a character vector of length=2 specifying the colors of the tips.
`col.edges` | a character vector of length=2 specifying the colors of the edges.
`col.root` | a character value specifying the color of the inferred root.
`plot.sspnames` | a single logical value specifying whether ssp names should be used to generate the plot.
`plot.subtree` | a single logical value specifying whether a sub-species tree should be used to generate the plot.
`plot.lcas` | a single logical value specifying whether a species tree should be generated mapping the positions of all possible roots.

### Value

a pdf file.

### Author(s)

Rodrigo Dalmolin, Mauro Castro

### References

Dalmolin RJ and Castro, MA. Geneplast: Evolutionary rooting using orthologous groups distribution. Journal Paper (in preparation), 2016.

### See Also

`groot`

### Examples

    #load datasets used for demonstration
    data(gpdata.gs)

    #create and object of class 'OGR' for H. sapiens
    ogr <- groot.preprocess(cogdata=cogdata, phyloTree=phyloTree, spid="9606", cogids=cogids)

    ## run the groot function
    ogr <- groot(ogr, nPermutations=100)

    ## this example plots NOG40170 in the phyloTree
    groot.plot(ogr,whichOG="NOG40170")

[Package geneplast version 1.16.0 Index]