dotchart.phylog {ade4} | R Documentation

## Representation of many quantitative variables in front of a phylogenetic tree

### Description

`dotchart.phylog` represents the phylogenetic tree and draws Cleveland dot plot of each variable.

### Usage

    dotchart.phylog(phylog, values, y = NULL, scaling = TRUE, ranging =
    TRUE, yranging = NULL, joining = TRUE, yjoining = NULL, ceti = 1, cdot =
    1, csub = 1, f.phylog = 1/(1 + ncol(values)), ...)

### Arguments

`phylog` | an object of class `phylog`
`values` | a vector or a data frame giving the variables
`y` | a vector which values correspond to leaves positions
`scaling` | if TRUE, data are scaled
`ranging` | if TRUE, dotplots are drawn with the same horizontal limits
`yranging` | a vector with two values giving the horizontal limits. If NULL, horizontal limits are defined by lower and upper values of data
`joining` | if TRUE, segments join each point to a central value
`yjoining` | a vector with the central value. If NULL, the central value equals 0
`ceti` | a character size for editing horizontal limits, used with `par("cex")*ceti`
`cdot` | a character size for plotting the points of the dot plot, used with `par("cex")*cdot`
`csub` | a character size for editing the names of variables, used with `par("cex")*csub`
`f.phylog` | a size coefficient for tree size (a parameter to draw the tree in proportion to leaves labels)
`...` | further arguments passed to or from other methods

### Author(s)

Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr

### See Also

`symbols.phylog` and `table.phylog`

### Examples

    # one variable
    tre <- c("((A,B),(C,D));")
    phy <- newick2phylog(tre)
    x <- 1:4
    par(mfrow = c(2,2))
    dotchart.phylog(phy, x, scaling = FALSE)
    dotchart.phylog(phy, x)
    dotchart.phylog(phy, x, joining = FALSE)
    dotchart.phylog(phy, x, scaling = FALSE,
     yjoining = 0, yranging = c(-1, 5))
    par(mfrow = c(1,1))

    # many variables
    data(mjrochet)
    phy <- newick2phylog(mjrochet$tre)
    tab <- data.frame(log(mjrochet$tab))
    dotchart.phylog(phy, tab, ceti = 0.5, csub = 0.6,
     cleaves = 0, cdot = 0.6)
    par(mfrow=c(1,1))

[Package ade4 version 1.7-13 Index]