Dear Dr. Revell,
I tried par(fg="green") and it kind of worked. It changed the curved
labels and their associated text to a color, but it only changed the
outline of the dots denoting marked nodes. Additionally, if I tried to
input a vector of colors equal to my number of groups (e.g.,
par(fg=c("red","green","blue","cyan","orange")), I get the error ""fg1" is
not a graphical parameter".
The same results are produced if I try par(col="green"). The command
par(col.lab="green") just turns the entire background of the figure green.
I also tried part(fill="green"), but got the warning message "In par(fill =
"green") : "fill" is not a graphical parameter". The command
par(bg="green') does nothing.
Sincerely,
Russell
On Mon, Apr 5, 2021 at 11:11 AM Liam J. Revell wrote:
> Dear Russell.
>
> I'm sorry that arc.cladelabels does not have the functionality that you
> want.
>
> Have you tried setting par(fg)? E.g.:
>
> par(fg="the color you want")
> arc.cladelabels(...)
> par(fg="black")
>
> You could also try par(col) or par(col.lab).
>
> Let me know if that works, if not I can see about adding the option you
> need to the function.
>
> All the best, Liam
>
> Liam J. Revell
> University of Massachusetts Boston [Assoc. Prof.]
> Universidad Católica de la Ssma Concepción [Adj. Res.]
>
> Web & phytools:
> http://faculty.umb.edu/liam.revell/, http://www.phytools.org,
> http://blog.phytools.org
>
> Academic Director UMass Boston Chile Abroad:
> https://www.umb.edu/academics/caps/international/biology_chile
>
> U.S. COVID-19 explorer web application:
> https://covid19-explorer.org/
>
> On 4/4/2021 10:36 PM, Russell Engelman wrote:
> > EXTERNAL SENDER
> >
> > Dear R-sig-phylo,
> >
> > I am a researcher who has been trying to plot a continuous trait map
> onto a
> > phylogeny using the phytools and ape packages in R. I have been trying to
> > denote specific clades using the arc.cladelabels function in phytools,
> but
> > I have also been trying to color-code the text, curve, and node for each
> of
> > the groups to make it easier to see which branches pertain to which
> clade.
> > However, I have been having a lot of trouble adjusting the properties of
> > the text and nodes created by arc.cladetools.
> >
> > Here is an example using the *Anolis *svl data that shows what I mean:
> >
> > ```
> > library(ape)
> > library(phytools)
> > anole.tree<-read.tree("
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2Feqg2015%2Fdata%2Fanole.tredata=04%7C01%7Cliam.revell%40umb.edu%7C017b93bf1ab74239149608d8f84157ed%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637532306822786314%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=NN6WMsldnLYZtuXWpndNA6ORhejdZbJdqDuNeI6PsY8%3Dreserved=0
> ")
> > svl <- read.csv("
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2Feqg2015%2Fdata%2Fsvl.csvdata=04%7C01%7Cliam.revell%40umb.edu%7C017b93bf1ab74239149608d8f84157ed%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637532306822796308%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=EA2P63ohsozCGtfU9hpg9k319zu168X%2BfmCZlOJ4cX4%3Dreserved=0
> ",
> > row.names=1)
> > svl <- as.matrix(svl)[,1]
> > fit <- fastAnc(anole.tree,svl,vars=TRUE,CI=TRUE)
> > obj<-contMap(anole.tree,svl,plot=FALSE)
> > nodes<-c(mrca(anole.tree)["equestris","noblei"],
> > mrca(anole.tree)["barahonae","barbatus"])
> > labels<-c("clade1","clade2")
> > plot(obj,type="fan",cex=5,fsize=0.5,lwd=5)
> > for(i in 1:length(nodes))
> >arc.cladelabels(text = labels[i],node = nodes[i],mark.node = TRUE,
> > ln.offset =
> > 1.39, col = c("green","red")[i], lab.offset =
> > 1.46, fsize = .5, orientation = "curved")
> > ```
> >
> > None of the calls I have tried for the arc.cladelabels function seem to
> be
> > able to adjust the color of the text labels the function creates (e.g.,
> > text.col, col.text, col.lab, etc), nor the color or size of the nodes
> when
> > mark.node = TRUE. The "col" call only affects the line drawn. Examining
> the
> > base code for arc.cladelabels finds that the color of the nodes is always
> > set to be red, and I have been unable to figure out how to alter it. I
> > could always write a custom function that copies arc.cladelabels but
> alters
> > the color function, but my concern is that this is part of an RMarkdown
> > document and as a result any alteration I make to the arc.cladelabels
> > function will not show up when another person knits the data (as it will
> > call on their copy of phytools).
> >
> > Alternatively I am wondering if it is possible to export the tree to
> ggtree
> > and add the nodes there, but I have noticed that ggtree does not allow
> for
> > arced clade labels and for some reason it also greatly extends the
> margins
> > of the plot beyond the margins of the graph when its equivalent of
> >
