table.phylog {ade4} | R Documentation |
This function gives a graphical display for viewing the numbers of a table by square sizes in front of the corresponding phylogenetic tree.
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$nodes), clabel.nod = 0, cleaves = 1, cnodes = 1, csize = 1, grid = TRUE, clegend = 0.75)
df |
: a data frame or a matrix |
phylog |
: an object of class |
x |
: a vector of values to position the columns |
f.phylog |
: a size coefficient for tree size (a parameter to draw the tree in proportion to leaves labels) |
labels.row |
: a vector of strings of characters for row labels |
clabel.row |
: a character size for the leaves labels, used with |
labels.col |
: a vector of strings of characters for columns labels |
clabel.col |
: a character size for the leaves labels, used with |
labels.nod |
: a vector of strings of characters for the nodes labels |
clabel.nod |
: a character size for the nodes labels, used with |
cleaves |
: a character size for plotting the points that represent the leaves, used with |
cnodes |
: a character size for plotting the points that represent the nodes, used with |
csize |
: a size coefficient for symbols |
grid |
: a logical value indicating whether the grid should be plotted |
clegend |
: a character size for the legend (if 0, no legend) |
The function verifies that sort(row.names(df))==sort(names(phylog$leaves))
.
If df
is a matrix the function uses as.data.frame(df)
.
Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr
symbols.phylog
for one variable
## 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)