Dear r-sig-phylo members,
I have a question about the usage of gradients in plot.phylo.
I thought it would be useful to visualize change on my trees by plotting
gradients from each tip/node to each tip/node. However, plot.phylo seems
to only want to plot uniform colors, and not gradients....
Here is my code (I know it's messy, but since I'm still working on it is
clearer for me):
library(ape)
library(plotrix)
rtree(15) -> tree
rnorm(15, mean = 0.5, sd = 0.15) -> data
ace(data, tree) -> results
data <- append(data,results$ace)
names(data) <- NULL
create.gradient <- function(i){
colorgrad01<-color.scale(seq(0,1,by=0.01), extremes=c("red","blue"))
tree$edge[i,1] -> x
tree$edge[i,2] -> y
print(x)
print(y)
data[x] -> z
data[y] -> z2
round(z, digits = 2) -> z
round(z2, digits = 2) -> z2
z*100 -> z
z2*100 -> z2
print(z)
print(z2)
colorgrad<-colorgrad01[z:z2]
colorgrad
}
out <- lapply(1:nrow(tree$edge), create.gradient)
so now all gradients for each of the 28 individuals are stored in the
object out. Then I try to plot it:
plot.phylo(tree, edge.color=c(out4[[1]], out4[[2]], out4[[3]],
out4[[5]], out4[[6]], out4[[7]], out4[[8]], out4[[9]], out4[[10]],
out4[[11]], out4[[12]], out4[[13]], out4[[14]], out4[[15]], out4[[16]],
out4[[17]], out4[[18]], out4[[19]], out4[[20]], out4[[21]], out4[[22]],
out4[[23]], out4[[24]], out4[[25]], out4[[26]], out4[[27]], out4[[28]]),
edge.width=5)
It plots fine, but I don't see the gradients, but just uniform colors
across the branches. I think it just takes the first color value of
each gradient? So - is it impossible to do this with plot.phylo? Or am I
overlooking something...?
Thanks!
Annemarie
--
Annemarie Verkerk, MA
Evolutionary Processes in Language and Culture (PhD student)
Max Planck Institute for Psycholinguistics
P.O. Box 310, 6500AH Nijmegen, The Netherlands
+31 (0)24 3521 185
http://www.mpi.nl/research/research-projects/evolutionary-processes
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