geo.legend | R Documentation |
Adds a geological legend to a plotted tree.
geo.legend(leg=NULL, colors=NULL, alpha=0.2, ...)
geo.palette()
leg |
a matrix with the starting & ending point of each plotted era in rows, & names of the time periods as rownames. |
colors |
a vector of colors for the time periods of the rows in |
alpha |
transparency level to apply to |
... |
optional arguments. |
The function geo.legend
adds a geological (or other temporal) legend to a plotted tree.
The function geo.palette
returns a geological time color palette to the user.
geo.legend
adds a visual element to a plotted tree and invisible returns an object of class geo.legend
containing the time periods and colors of the painted legend.
geo.palette
simply returns a geological timescale color palette as an object of class "geo.palette"
.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
data(anoletree)
## rescale tree to 50 ma total depth
anoletree<-rescale(anoletree,model="depth",depth=50)
## plot phylogeny
plotTree(anoletree,ylim=c(-0.16,1)*Ntip(anoletree),
ftype="i",lwd=1,fsize=0.5)
## add geological color legend
obj<-geo.legend()
par(mar=c(5.1,4.1,4.1,2.1))
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