dotchart.phylog: Representation of many quantitative variables in front of a...

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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 [e-mail]

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))

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.