Woops.
Solution: pull development version of /phytools/ from GitHub.
library(remotes)
install_github("liamrevell/phytools")
That should fix it. (Not sure what got broken, but evidently I fixed it
on GitHub & forgot about it.)
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 9:53 AM, Joseph Brown wrote:
>
>
> You don't often get email from [email protected]. Learn why this is
> important <https://aka.ms/LearnAboutSenderIdentification>
>
>
> CAUTION: EXTERNAL SENDER
> That code doesn't seem to work?
>
> Error in plot.xy(xy.coords(x, y), type = type, ...) : invalid line type
> 4.
> plot.xy(xy.coords(x, y), type = type, ...)
> 3.
> lines.default(a, b, col = colors[names(tree$maps[[i]])[j]], lwd = lwd,
> lty = lty[names(tree$maps[[i]])[j]], type = type)
> 2.
> lines(a, b, col = colors[names(tree$maps[[i]])[j]], lwd = lwd,
> lty = lty[names(tree$maps[[i]])[j]], type = type)
> 1.
> phenogram(mammal_cmap$tree, lnBodyMass, colors = mammal_cmap$cols,
> spread.cost = c(1, 0), fsize = 0.8, lwd = 3, ftype = "i")
>
> My info:
> R version 4.3.3 (2024-02-29)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 24.04.3 LTS
>
> other attached packages:
> [1] phytools_2.4-4 maps_3.4.3 ape_5.8-1
>
> JWB
>
> On Tue, Sep 9, 2025 at 9:44 AM Liam J. Revell via R-sig-phylo
> <[email protected]> wrote:
>
> 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/
> <http://faculty.umb.edu/liam.revell/>
> Book: Phylogenetic Comparative Methods in R
> <https://press.princeton.edu/books/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:
> > [You don't often get email [email protected]. Learn why
> this is important athttps://aka.ms/LearnAboutSenderIdentification
> <http://aka.ms/LearnAboutSenderIdentification> ]
> >
> > CAUTION: EXTERNAL SENDER
> >
> > 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
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-phylo mailing list [email protected]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
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> athttp://www.mail-archive.com/[email protected]/
> <http://www.mail-archive.com/[email protected]/>
> [[alternative HTML version deleted]]
>
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