table.phylog {ade4}R Documentation

Plot arrays in front of a phylogenetic tree

Description

This function gives a graphical display for viewing the numbers of a table by square sizes in front of the corresponding phylogenetic tree.

Usage

table.phylog(df, phylog, x = 1:ncol(df), f.phylog = 0.5,
 labels.row = gsub("[_]", " ", row.names(df)), clabel.row = 1,
 labels.col = names(df), clabel.col = 1,
 labels.nod = names(phylog$nodes), clabel.nod = 0, cleaves = 1,
 cnodes = 1, csize = 1, grid = TRUE, clegend = 0.75)

Arguments

df : a data frame or a matrix
phylog : an object of class 'phylog'
x : a vector of values to position the columns
f.phylog : a size coefficient for tree size (a parameter to draw the tree in proportion to leaves labels)
labels.row : a vector of strings of characters for row labels
clabel.row : a character size for the leaves labels, used with par("cex")*clabel.row. If zero, no row labels are drawn
labels.col : a vector of strings of characters for columns labels
clabel.col : a character size for the leaves labels, used with par("cex")*clabel.col. If zero, no column labels are drawn
labels.nod : a vector of strings of characters for the nodes labels
clabel.nod : a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
cleaves : a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
cnodes : a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
csize : a size coefficient for symbols
grid : a logical value indicating whether the grid should be plotted
clegend : a character size for the legend (if 0, no legend)

Details

The function verifies that sort(row.names(df))==sort(names(phylog$leaves)). If df is a matrix the function uses as.data.frame(df).

Author(s)

Daniel Chessel
S├ębastien Ollier ollier@biomserv.univ-lyon1.fr

See Also

symbols.phylog for one variable

Examples

## Not run: 
data(newick.eg)
w.phy <- newick2phylog(newick.eg[[9]])
w.tab <- data.frame(matrix(rnorm(620), 31, 20))
row.names(w.tab) <- sort(names(w.phy$leaves))
table.phylog(w.tab, w.phy, csi = 1.5, f = 0.5,
 clabel.n = 0.75, clabel.c = 0.5)

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: table.phylog
> ### Title: Plot arrays in front of a phylogenetic tree
> ### Aliases: table.phylog
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(newick.eg)
> w.phy <- newick2phylog(newick.eg[[9]])
> w.tab <- data.frame(matrix(rnorm(620), 31, 20))
> row.names(w.tab) <- sort(names(w.phy$leaves))
> table.phylog(w.tab, w.phy, csi = 1.5, f = 0.5,
+  clabel.n = 0.75, clabel.c = 0.5)
> 
> 
> 
> 
> 

[Package ade4 Index]