Some background in case I have got the wrong idea here. I have 240 amino acid sequences and want to see how closely related these sequences are (as well as visualising it), and how similar they are between different strains of bacteria. I have a data frame with the sequences as well as a column indicating to which strain each sequence belongs.

I have calculated a distance matrix after aligning the amino acid sequences in DECIPHER using the following code:

aa_aligned <- AlignSeqs(NZ_50_mature_D0.4_first50aa)

d <- DistanceMatrix(aa_aligned)

I then clustered them based on this matrix using IdCluster:

c <- IdClusters(d, show=TRUE, verbose = T)

This gives a tree, but with 240 sequences it is hard to read the names of the id's to then relate back to which strain they belong.

I would like to be able to colour the tree based on the "strain" column in my data frame. This way it will be easier visually to see if the sequences form the same strains cluster together. Is this possible?

Note: there are 50 "strains" so a key would be useful too.

If there is a better way t achieve what I am trying to do then any advise is welcome, I am still new to this kind of analysis in R,

Thank you.

Thanks for your interest in DECIPHER.  Without your sequences it will be hard to provide an exact answer, but this should hopefully get you started...

Here is some artificial data for this example:

aa <- AAStringSet(c(Strain1="NLK", Strain2="NLV", Strain3="NIL"))

aa_aligned <- AlignSeqs(aa)

d <- DistanceMatrix(aa_aligned)

So far this is similar to what you wrote. Next, you will need to get the dendrogram:

tree <- IdClusters(d, type="dendrogram")

I am going to assume that you have a vector of colors named by the strain labels:

colors <- c(Strain1="red", Strain2="blue", Strain3="green")

Then you can color the labels or edges based on the strain name.

tree_colored <- dendrapply(tree,
    FUN=function(n) {
        if(is.leaf(n))
            attr(n, "nodePar") <- list(lab.col=colors[attr(n, "label")], pch=NA)
        n
    })

The key line above is:

attr(n, "nodePar") <- list(lab.col=colors[attr(n, "label")], pch=NA)

This could be modified to color only the leaves of the tree:

attr(n, "edgePar") <- list(col=colors[attr(n, "label")])

See ?dendrogram for more options.  Now, we can draw the plot:

plot(tree_colored)

You can add a key with the legend function:

legend("topright", names(colors), text.col=colors)

I hope that helps.