groot.plot: Plot the inferred evolutionary root of a given OG or the map...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/AllPlots.R

Description

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

Usage

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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

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#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")

geneplast documentation built on Nov. 1, 2018, 2:27 a.m.