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 ollier@biomserv.univ-lyon1.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 1.4-10 Index]