ade4: table.phylog – R documentation

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table.phylog

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
Sébastien Ollier sebastien.ollier@u-psud.fr

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)

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release