blueraleigh
commented
10 years ago The documentation is up to date now and will answer some these questions. I changed some things to allow plotting subtrees while preserving the color mapping relative to the entire tree. Not sure why specifying a list used to work, but any vector of three colors is supported. I think it will catch any arguments that result in "colpalette not found error" and give a more informative message. All examples work.
I'm finding plot.bammdata colors a little confusing.
First, plotting function as defined in the help file suggests you can do color interpolation (pal = c("darkgreen","yellow2","red")). But that's not the actual default function call (which used 'set1'.
Is color interpolation generally supported for any user-defined vector of colors?
As far as I can tell, it looks like this no longer takes a list of colors
plot.bammdata(ed, method='polar', pal=list(c('blue', 'gray', 'red'))) used to work for me but now looks like it uses vectors
Can the "colpalette not found" error ONLY arise if RColorBrewer is not loaded? This seems like a common and cryptic error I get - would be worth making this somehow less difficult to understand for general user.
Also, I get the following error running the example code: Error in tau - (ephy$end[i]/tH - tail(segs, 1)) : 'tau' is missing
(all the examples will have to work without error or this will get rejected from CRAN)