Wahoo! The code now works! I installed phytools from Liam's github page and
restarted R. I spent an embarrassing amount of time trying to
troubleshoot this yesterday. I was not about to do it for a second day ha.
Thank you all! I really appreciate all the quick and helpful feedback!
Best,
Lindsey
On Tue, Sep 9, 2025 at 10:15 AM Michael Zyphur <mzyp...@instats.org> wrote:
> Hi Joseph and Liam
>
> The error trace shows that phenogram is trying to access
> lty[names(tree$maps[[i]])[j]] and failing, which may indicate a
> version-specific bug in how phytools handles the colors argument — in
> phytools v2.4-4 there may be a bug where phenogram incorrectly handles line
> types when colors from contMap are provided. It tries to match line types
> to color segments but passes an invalid value, triggering the 'invalid line
> type' error. Here are a few ideas:
> A quick fix could be to add lty=1 to explicitly set the line type
>
> phenogram(obj$tree, fineness_ratio, colors=obj$cols, spread.labels=TRUE,
> spread.cost=c(1,0), fsize=0.3, ftype="reg", lwd=1.25, lty=1,
> ylab="Fineness ratio", ylim=c(0,2.5))
>
> Update phytools:
>
> install.packages("phytools")
> # Then restart R session
>
> Try the dev version from GitHub in case it works?
>
> remotes::install_github("liamrevell/phytools")
>
>
> Best wishes
>
> Michael Zyphur
> Professor and Director
> Instats | instats.org
> Follow Instats: Bluesky <https://bsky.app/profile/instats.bsky.social>
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>
>
> On Tue, 9 Sept 2025 at 23:54, Joseph Brown <josep...@umich.edu> wrote:
>
> > That code doesn't seem to work?
> >
> > Error in plot.xy(xy.coords(x, y), type = type, ...) : invalid line type
> > 4.
> > plot.xy(xy.coords(x, y), type = type, ...)
> > 3.
> > lines.default(a, b, col = colors[names(tree$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$cols,
> > spread.cost = c(1, 0), fsize = 0.8, lwd = 3, ftype = "i")
> >
> > My info:
> > R version 4.3.3 (2024-02-29)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 24.04.3 LTS
> >
> > other attached packages:
> > [1] phytools_2.4-4 maps_3.4.3 ape_5.8-1
> >
> > JWB
> >
> > On Tue, Sep 9, 2025 at 9:44 AM Liam J. Revell via R-sig-phylo <
> > r-sig-phylo@r-project.org> wrote:
> >
> > > Hi Lindsey.
> > >
> > > To be honest, I don't see a problem with your code -- unless your R
> > > graphical device does not support lwd=1.25. (That's the only thing I
> > > could think of without being able to reiterate your analysis & debug
> it.)
> > >
> > > Here's a fully worked example of the same type of plot that uses data
> > > packaged with /phytools/.
> > >
> > > library(phytools)
> > > data("mammal.tree")
> > > data("mammal.data")
> > >
> > > lnBodyMass<-setNames(log(mammal.data$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/
> > > 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:
> > > > [You don't often get email fromlmdeh...@umich.edu. Learn why this is
> > > important athttps://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]]
> > > >
> > > > _______________________________________________
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> > >
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> > >
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>
--
Lindsey DeHaan
Ph.D. Candidate
Department of Earth and Environmental Sciences
University of Michigan
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