Hi Lindsey.
To be honest, I don't see a problem with your code -- unless your R
graphical device does not support lwd=1.25. (That's the only thing I
could think of without being able to reiterate your analysis & debug it.)
Here's a fully worked example of the same type of plot that uses data
packaged with /phytools/.
library(phytools)
data("mammal.tree")
data("mammal.data")
lnBodyMass<-setNames(log(mammal.data$bodyMass),
rownames(mammal.data))
mammal_cmap<-contMap(mammal.tree,lnBodyMass,
plot=FALSE)
mammal_cmap<-setMap(mammal_cmap,hcl.colors(n=100))
plot(mammal_cmap) ## standard contMap plot
dev.off()
phenogram(mammal_cmap$tree,lnBodyMass,
colors=mammal_cmap$cols,
spread.cost=c(1,0),fsize=0.8,lwd=3,
ftype="i")
If this doesn't help you figure out what's going wrong, please feel free
to send me your data & code (or, better yet, a saved R workspace) and
I'd be happy to troubleshoot it here.
Best wishes, Liam
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/, 2022)
On 9/9/2025 9:27 AM, Lindsey Dehaan wrote:
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>
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>
> Hi all,
>
> I have a quick question that I think someone could answer for me in a
> couple minutes rather than spend 2 hours of my day trying to figure it out.
>
> I want to make a phenogram (or traitagram) showing the evolutionary
> trajectory of a trait of a group of fishes. While this would be
> sufficient enough for the figure, I think it would be neat to map the color
> scheme of the continuous character produced by contMap() onto the branches
> of the phenogram. However, I am running into an error and I am not exactly
> sure how to fix it. The phenogram plots no problem, the contMap plots no
> problem, but I am having trouble combining the two outputs. The error I
> keep getting is "Error in plot.xy(xy.coords(x, y), type = type, ...) :
> invalid line type"
>
> I have tried to tweak the code so many times to get around this error but I
> am finally at a loss. I would appreciate any pointers or tips anyone
> could throw my way. My code is below and I am happy to share the data if
> needed.
>
> Best,
> Lindsey
>
>> phenogram(locate_fossil_phy, fineness_ratio, fsize = 0.5, ftype = "reg",
> xlab=NULL, ylab="log Fineness Ratio")
>
> #Create contMap of continuous trait
>> obj<-contMap(locate_fossil_phy,fineness_ratio,plot=TRUE, res=50)
>> plot(obj,legend=0.75*max(nodeHeights(locate_fossil_phy)),
> fsize=c(0.2,.8), lwd=2, label.offset=2,
> outline=FALSE, ftype="off", fsize=0.66)
>
> #Change Colors
>> obj <- setMap(obj, c("#0000FF","#6600CC", "#FF0000", "#990000")) #Blue to
> Red
>
> # Plot phenogram with obj$colors
> phenogram(obj$tree,fineness_ratio,colors=obj$cols,spread.labels=TRUE,
> spread.cost=c(1,0),fsize=0.3,ftype="reg",lwd=1.25,
> ylab="Fineness ratio", ylim=c(0,2.5))
>
>
>
> *Error in plot.xy(xy.coords(x, y), type = type, ...) : invalid line type*
> *-- *
> Lindsey DeHaan
> Ph.D. Candidate
> Department of Earth and Environmental Sciences
> University of Michigan
>
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