[BioC] ColSideColors

[Wolfgang Huber]

Dear Sabah,

have a look at this:
http://tolstoy.newcastle.edu.au/R/e2/help/07/09/25712.html
there is a code example, I repeat it here for your convenience:

library("lattice")
library("latticeExtra")

hc1 = hclust(dist(USArrests, method = "canberra"))
hc1 = as.dendrogram(hc1)
ord.hc1 = order.dendrogram(hc1)

hc2 = reorder(hc1, state.region[ord.hc1])
ord.hc2 = order.dendrogram(hc2)

region.colors = trellis.par.get("superpose.polygon")$col

levelplot(t(scale(USArrests))[, ord.hc2],
  scales = list(x = list(rot = 90)),
    colorkey = FALSE,
    legend = list(right =
        list(fun = dendrogramGrob,
           args =
            list(x = hc2, ord = ord.hc2,
                 side = "right", size = 10, size.add= 0.5,
                 add = list(
                   rect = list(col = "transparent",
                     fill = region.colors[state.region]),
                   rect = list(col = "transparent",
                     fill = region.colors[rev(state.region)])),
                        type = "rectangle"))))



Generally, the heatmap function from the base package is quite
inflexible, and I doubt that it would be easy or worthwhile to make it
do what you propose. The suggestion that Deepayan is making above will
require a certain amount of investment of your time in understanding how
the lattice graphics package works, but it is worth it!

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber



Sabah khalid ha scritto:
> Dear all,
> 
> I have been using R for a short time now and I am having a little difficulty
> with the following.  Whilst I am able to generate one row of ColSideColors
> above my heatmap, I would like to generate 2 ColSideColors each representing
> different information.
> 
> So far I have:
> 
> #the column one from my headers file is used as ColSideColors
> mycols2 <- as.character(as.numeric(headers$one));
> #I would also like to present this column (two) aswell, but do not know
> how..
> mycols3<-as.character(as.numeric(headers$two));
> 
> heatmap(mymatrix,ColSideColors = mycols2,col= greenred(256));
> 
> How can I incorporate mycols3 into the heatmap function as well?  I am
> thinking it must be a syntax issue which I am not too familiar with yet.
> 
> Thank you to anyone who can help me
> 
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