R: Plot arrays in front of a phylogenetic tree

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
Sébastien Ollier sebastien.ollier@u-psud.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)

[Package ade4 version 1.7-16 Index]