[R] Coloring leaves in Dendrogram according to gene names

[PQuery]

Hello,

I am a new R user and have a question regarding dendrogram coloring.
I would like to color each leaf in the dendrogram (dhc) according to a
specific criterion. For me this criterion is the gene name.
For this, I created a data.frame with 2 variables: The gene name and the
corresponding color.


Using the following function, adapted from "dendrapply {stats}", I still
have the same color for the leaves.
Using the standard function (with the my_colors[i]), I do have the leaves of
different colors !!!

The structure of "my_colors[i]" is the same as the structure of "color" !!!

Do you have any idea on what is going wrong ?

Many thanks for your help,


targetGenes<-length(unique(bm$Target)) #Getting the number of unique target
genes

my_colors<-rainbow(targetGenes) #Creating a vector of colors for each gene

gene2color<-data.frame(gene=unique(bm$Target), color=my_colors) #Creating
the data.frame

dhc<-as.dendrogram(fit.x) #the dendrogram using the hclust object (fit.x)

local({
  colLab <<- function(n) {
      if(is.leaf(n)) {
        a <- attributes(n)
        crm <- as.numeric(a$label)
        gene <- as.character(bm[which(bm$CRM_ID==crm),5])
        color <- as.character(gene2color[which(gene2color$genes==gene),2])
        i <<- i+1
        attr(n, "nodePar") <-
          # c(a$nodePar, list(lab.col = my_colors[i], lab.font= i%%3))
          c(a$nodePar, list(lab.col = color))
      }
      n
  }
  my_colors <- grDevices::rainbow(attr(dhc,"members"))
  i <- 0
  })

dL <- dendrapply(dhc, colLab)

op <- par(mfrow=2:1)

plot(dhc)
plot(dL)pierre.khoueiry at embl.de
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