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
S├ębastien 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))

Worked out examples


> library(ade4)
> ### Name: dotchart.phylog
> ### Title: Representation of many quantitative variables in front of a
> ###   phylogenetic tree
> ### Aliases: dotchart.phylog
> ### Keywords: hplot
> 
> ### ** 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 Index]