Representation of many quantitative variables in front of a phylogenetic tree

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

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))