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/ > 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 [email protected]. 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]] > > > > _______________________________________________ > > R-sig-phylo mailing list [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive athttp:// > www.mail-archive.com/[email protected]/ > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
