R - Add a colored side bar to a heatmap.2

Question

I have several problems with R. I am trying to plot a heatmap with both row and col dendrograms, till here everything is okay. Now I want to add a side bar using ColSideColors. The colors depends of the proteins' domains, I have these data in a different vector called domains, containing the names of the proteins and the colors associated to the domains. I have already check, each domain has a color, everything is fine. But when I add the side bar to the plot, it seems that the color are not in the correct order. How can I fix this ? Please find the code bellow :

domains <- read.table("pubchem_proteins_domains.csv", sep = ",", dec  = ".", quote = "\"")
domains$values  <- (domains$V2 - min(domains$V2))/(max(domains$V2) - min(domains$V2))
domains$gray <- gray(domains$values)

head(domains)

                                                                             V1
1           P10275.ANDR_HUMAN.Androgen.receptor.OS.Homo.sapiens.GN.AR.PE.1.SV.2
2       P00915.CAH1_HUMAN.Carbonic.anhydrase.1.OS.Homo.sapiens.GN.CA1.PE.1.SV.2
3       P00918.CAH2_HUMAN.Carbonic.anhydrase.2.OS.Homo.sapiens.GN.CA2.PE.1.SV.2
4       P22748.CAH4_HUMAN.Carbonic.anhydrase.4.OS.Homo.sapiens.GN.CA4.PE.1.SV.2
5    P21554.CNR1_HUMAN.Cannabinoid.receptor.1.OS.Homo.sapiens.GN.CNR1.PE.1.SV.1
6 P24941.CDK2_HUMAN.Cyclin-dependent.kinase.2.OS.Homo.sapiens.GN.CDK2.PE.1.SV.2
  V2 values    gray
1 16   0.60 #999999
2  7   0.24 #3D3D3D
3  7   0.24 #3D3D3D
4  7   0.24 #3D3D3D
5  2   0.04 #0A0A0A
6 22   0.84 #D6D6D6

mol_distances <- read.table("pubchem_molecular_distances.csv", header = T, sep = ",")
row.names(mol_distances) <- mol_distances[,1]
mol_distances <- mol_distances[,-c(1)]

alignment <- read.alignment(file = "pubchem_alignment.txt", format = "clustal")
prot_distances <- dist.alignment(alignment)

hc_mol <- hclust(as.dist(mol_distances), method="ward")
hc_prot <- hclust(as.dist(prot_distances), method="ward")

heatmap.2(dat_mat, 
Rowv = as.dendrogram(hc_prot), 
Colv = as.dendrogram(hc_mol), 
RowSideColors=domains$gray[domains$proteins_name],
dendrogram = "both",
scale = "none",
margins = c(12,24),
key = TRUE,
keysize = 1.0,
col = rainbow(512, start = 1, end = 0.4), 
density.info="density", 
denscol = "black",
xlab="Compounds", 
ylab="Targets", main="X Activity Profile",
trace ="none")

Beside, I could not find another function to do similar things in R for colors, can i do the same with rainbow ?

Thank you Regards Deuterium

Answer 1

Well, I solved my problem, it seems that they were several problem within my data sets, meaning that the R script is correct. Now the colors are assigned to the correct proteins. But I still don't know if it is possible to do similar side bar using other colors than gray, to make it more clear.

Thank you Deuterium