To see how these options can be used, lets first plot using the default values. The current tree has a three state mapped character, with states 1, 2, and 3.
> cols<-c("blue","yellow","red"); names(cols)<-c(1,2,3)
> plotSimmap(mtree,cols)
The first line is to create a vector with the colors we want; and the second line plots the tree. We get:
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgiK2AYM8MdQBkFVGmQhPmPambuyVuKBPsyHw5wm0zfLuQd5evxEr188IzkuZBg-Ihcv-vraHC8pcd7Lyo065BWX3tHKkpqAD1ojUDHTip-8HP0V7GYGEW_MnRW0ATK_d8W6bZgtHwbtROJ/s400/tree1.7.9.11.png)
Now, let's get rid of the circles and plot the lines a little bit more thickly. (This is more like what we'd see if we used FigTree, for instance.) We can change the font to italics as well if we want:
> plotSimmap(mtree,cols,lwd=5,pts=F,ftype="i")
Now we get:
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgls8l87eOFzdbsvlzXFoBPoyaJMW6WE5wMgy7t3JU2Pi9FrAnxLY8ppZhDHbdkbCyOdRWfcdEnYhXrxGVkD5jTKgDd8zNG_ukgYEoCN5Fy8QH9RJgdEiVGQnF_4J-cZbM4OUFkMOU7jZwq/s400/tree2.7.9.11.png)
Updates are in the newest version (v0.4) of this function as well in the latest alpha version of the "phytools" package (available here)
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