I don't know how to accomplish that in R, but in QGIS, you can use the
Topocolours plugin to accomplish that.

Hope this helps

2011/4/4 Karl Ove Hufthammer <karl@huftis.org>

> It’s sometimes useful to visualise maps with colours for each
> polygon, but where adjacent polygons have different colours.
>
> I recently had to do this, and hope the resulting code may be
> of use to others on this list. Note that the code uses a quick
> and simple greedy algorithm, which is not guaranteed to find
> a colouring using the *fewest* number of colours.
>
> It is *possible* to colour every map using at most four colours
> (try searching for ‘four colour theorem’ in your favourite search
> engine), but finding the optimal colouring isn’t easy, and an
> algorithm implementing this would be much more complicated, and
> in some cases rather slow. In practice, the greedy algorithm
> usually works very well. Note that sometimes it helps to order
> the polygons in some systematic way first, e.g., by the number
> of neighbours (the polygon with most neighbours first); see the
> example at the end.
>
> I would appreciate any suggestions for improvements to the code.
>
> # Generate colour numbers (indices) for colouring maps
> generateMapColours=function(x) {
>        nb=spdep::poly2nb(x)   # Generate neighbours lists
>        n=length(x)            # Number of polygons
>        cols=numeric(n)        # Initial colouring
>        cols[1]=1              # Let the first polygon have colour 1
>        cols1n=1:n             # Available colour indices
>        for(i in 2:n)
>                cols[i]=which.min(cols1n %in% cols[nb[[i]]])
>        cols
> }
>
> ## Example
> library(rgdal)    # Needed for maps in EPSG 4326 not to be interpreted as
> projected
> library(maps)     # For map data
> library(maptools) # For converting map data to ‘sp’ objects
>
> # Fetch a map
> x.map = map("state", fill=TRUE, col="transparent", plot=FALSE)
> x.sp = map2SpatialPolygons(x.map, x.map$names,
> proj4string=CRS("+init=epsg:4326"))
>
> # Plot the map with the calculated colours
> cols = generateMapColours(x.sp) # Generate the colour indices
> ncols = max(cols)               # Number of colours used
> library(RColorBrewer)           # Nice colour palettes for maps
> pal = brewer.pal(ncols, "Set1") # Try ‘display.brewer.all()’ for some
> alternative palettes
> plot(x.sp, col=pal[cols])       # Plot the map
>
> # Ordering the polygons may help.
> # For instance, running the colouring algorithm
> # on the following produces a four-colouring.
> nb = spdep::poly2nb(x.sp)
> ord = order(sapply(nb, length), decreasing=TRUE)
> x.sp = x.sp[ord,]
>
> --
> Karl Ove Hufthammer
>
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