fancyTree {phytools} | R Documentation |
This function plots different types of phylogenetic trees. If type="extinction"
(or any unambiguous abbreviation) the function will plot a tree in which branches preceding the MRCA of all extant taxa and branches leading only to extnct lineages are plotted with dashed red lines. If type="traitgram3d"
the function will plot a three dimensional traitgram (that is, a projection of the tree into three dimensional morphospace where two dimensions are the phenotypic trait and the third axis is time since the root). In this case, the additional argument X
, a matrix containing the tip values of all species (with species IDs as row names) should be supplied. Optionally, the user can also supply the matrix A
, which contains the ancestral states in the tree with rows labeled by node number. If type="droptip"
the function will create a two panel figure in which the first panel is the tree with lineages to be pruned highlighted; and the second panel is the pruned tree. In this case, the additional argument tip
, the tip name or vector of tip names to be dropped, must be supplied. If type="densitymap"
, a posterior probability density "heat-map" is created based on a set of trees in a "multiPhylo"
object containing a binary [0,1] mapped character. (See densityMap
for additional optional arguments if type="densitymap"
.) If type="contmap"
, reconstructed continuous trait evolution is mapped on the tree. Again, see contMap
for additional arguments if type="contmap"
. If type="phenogram95"
a 95-percent phenogram is plotted using transparency to visualize uncertainty at ancestral nodes and along branches. Most of the options of phenogram
are available. Finally, if type="scattergram"
a phylogenetic scatter plot matrix containing contMap
style trees on the diagonal and phylomorphospace
plots in non-diagonal panels is produced. For type="scattergram"
a trait matrix X
must be supplied. The only additional arguments available for this type are fsize
, colors
, and label
. (See phylomorphospace
for details.) Presently only type="traitgram3d"
uses the list control
which can be supplied the same set of control parameters as phylomorphospace3d
, as well as the control parameter maxit
which will be passed to anc.ML
. Finally, the optional argument hold
will be passed to multiple methods if supplied. It is a logical value that indicates whether or not the output to the graphical device should be held using dev.hold
before plotting (defaults to hold=TRUE
).
fancyTree(tree, type=c("extinction","traitgram3d","droptip","densitymap", "contmap","phenogram95","scattergram"), ..., control=list())
tree |
a phylogenetic tree in |
type |
the type of special plot to create. See Description. |
... |
arguments to be passed to different methods. |
control |
a list of control parameters, depending on |
This function plots different types of phylogenetic trees. For type="droptip"
the function also returns the pruned tree.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
contMap
, densityMap
, drop.tip
, phenogram
, phylomorphospace3d
, plot.phylo
, plotSimmap
# plot tree with extinction set.seed(10) tree<-pbtree(b=1,d=0.4,t=4) fancyTree(tree,type="extinction") ## Not run: # plot 3D traitgram tree<-pbtree(n=50,scale=10) Y<-sim.corrs(tree,vcv=matrix(c(1,0.75,0.75,1),2,2)) fancyTree(tree,type="traitgram3d",X=Y,control=list(spin=FALSE)) # plot with internal nodes from simulation Y<-sim.corrs(tree,vcv=matrix(c(1,0.75,0.75,1),2,2),internal=TRUE) B<-Y[length(tree$tip)+1:tree$Nnode,]; Y<-Y[1:length(tree$tip),] fancyTree(tree,type="traitgram3d",X=Y,A=B,control=list(simple.axes=TRUE,spin=FALSE)) ## End(Not run) # plot with dropped tips tree<-pbtree(n=30) tips<-sample(tree$tip.label)[1:10] pruned<-fancyTree(tree,type="droptip",tip=tips) ## Not run: # plot 95-percent CI phenogram tree<-pbtree(n=30) x<-fastBM(tree) fancyTree(tree,type="phenogram95",x=x) ## End(Not run)