Palette specification

[kingaa]

Palette specification

[kingaa]

But by default, palette=rainbow. See

ouch/R/plot.R

Line 150 in 3dec2ce

palette = rainbow,

[mbutler808]

Yes, I saw that. Sorry. I guess we want default palette = NULL, and if (is.null(palette)) palette=rainbow( length(levs)) ?

[mbutler808]

Or is

if (palette==rainbow) palette <- rainbow(length(levs))

a valid check? Otherwise use the vector specified ?

[mbutler808]

So I tried changing the default palette = rainbow in an tree plot, and it had no effect. I thought that rainbow(length(levs)) would return a vector of hex color codes, so I tried writing a dummy function 'mypal' that would return the same type of object:

col2hex <- function(cc) {rgb(col2rgb(cc)[1], col2rgb(cc)[2], col2rgb(cc)[3], maxColorValue=255)}

mypal <- function(x){return(c(col2hex("black"), col2hex("blue"), col2hex("purple")))}

data(bimac)
tree <- with(bimac,ouchtree(node,ancestor,time/max(time),species))

plot(tree,regimes=bimac["OU.LP"], palette=mypal)   # no effect
plot(tree,regimes=bimac["OU.LP"], palette= c("black", "blue", "purple"))   # no effect

I don't understand why specifying palette does nothing. It is a parameter to the plot function. Is it masked some how?

[kingaa]

Are you running the plotting branch? It works for me. Will merge the plotting branch in when we are finished with it.

[kingaa]

I've merged these changes to the master branch. Please have a look.

[mbutler808]

Thank you! It does work. Sorry for the delay.
Had figured out how to install from branch yesterday, lol. But I didnʻt have time to reply. It works but itʻs kind of awkward:

plot(tree, regimes=bimac["OU.LP"], palette=function(x)return(c("blue", "turquoise", "pink")))

Was the simplest implementation I could find. How about if we could also supply a vector? in tree.plot.internal:

  ifelse (class(palette)=="function", palette(length(levs)), palette) 

Then a vector could be supplied.

[kingaa]

Will do.