I have a numeric matrix in R with 24 rows and 10,000 columns. The row names of this matrix are basically file names from which I have read the data corresponding to each of the 24 rows. Apart from this I have a separate factor list with 24 entires, specifying the group to which the 24 files belong. There are 3 groups - Alcohols, Hydrocarbon and Ester. The names and the corresponding group to which they belong look like this:
> MS.mz
[1] "int-354.19" "int-361.35" "int-368.35" "int-396.38" "int-408.41" "int-410.43" "int-422.43"
[8] "int-424.42" "int-436.44" "int-438.46" "int-452.00" "int-480.48" "int-648.64" "int-312.14"
[15] "int-676.68" "int-690.62" "int-704.75" "int-312.29" "int-326.09" "int-326.18" "int-326.31"
[22] "int-340.21" "int-340.32" "int-352.35"
> MS.groups
[1] Alcohol Alcohol Alcohol Alcohol Hydrocarbon Alcohol Hydrocarbon Alcohol
[9] Hydrocarbon Alcohol Alcohol Alcohol Ester Alcohol Ester Ester
[17] Ester Alcohol Alcohol Alcohol Alcohol Alcohol Alcohol Hydrocarbon
Levels: Alcohol Ester Hydrocarbon
I wanted to generate a dendrogram to look how the data in the matrix can be clustered. So, I used the following commands:
require(vegan)
dist.mat<-vegdist(MS.data.scaled.transposed,method="euclidean")
clust.res<-hclust(dist.mat)
plot(clust.res)
and I got a dendogram. Now I want to color the file names in the dendrogram according to the group they belong to i.e Alcohol, Hydrocarbon or Ester. I looked at different examples posted on the forum like
Label and color leaf dendrogram in r
Label and color leaf dendrogram in R using ape package
, but could not implement it for my data. I am not sure how to correlate row.names with the MS.groups to get the colored names in the dendrogram.
On generating the tree using dendextend (as explained in https://nycdatascience.com/wp-content/uploads/2013/09/dendextend-tutorial.pdf), I get the following tree
Here is the code used to generate it:
require(colorspace)
d_SIMS <- dist(firstpointsample5[,-1])
hc_SIMS <- hclust(d_SIMS)
labels(hc_SIMS)
dend_SIMS <- as.dendrogram(hc_SIMS)
SIMS_groups <- rev(levels(firstpointsample5[, 1]))
dend_SIMS <- color_branches(dend_SIMS, k = 3, groupLabels = SIMS_groups)
is.character(labels(dend_SIMS))
plot(dend_SIMS)
labels_colors(dend_SIMS) <- rainbow_hcl(3)[sort_levels_values(as.numeric(firstpointsample5[,1])[order.dendrogram(dend_SIMS)])]
labels(dend_SIMS) <- paste(as.character(firstpointsample5[, 1])[order.dendrogram(dend_SIMS)],"(", labels(dend_SIMS), ")", sep = "")
dend_SIMS <- hang.dendrogram(dend_SIMS, hang_height = 0.1)
dend_SIMS <- assign_values_to_leaves_nodePar(dend_SIMS, 0.5,"lab.cex")
par(mar = c(3, 3, 3, 7))
plot(dend_SIMS, main = "Clustered SIMS dataset\n (the labels give the true m/z groups)",horiz = TRUE, nodePar = list(cex = 0.007))
legend("topleft", legend = SIMS_groups, fill = rainbow_hcl(3))
I suspect the function you are looking for is either color_labels
or get_leaves_branches_col
. The first color your labels based on cutree
(like color_branches
do) and the second allows you to get the colors of the branch of each leaf, and then use it to color the labels of the tree (if you use unusual methods for coloring the branches (as happens when using branches_attr_by_labels
). For example:
# define dendrogram object to play with:
hc <- hclust(dist(USArrests[1:5,]), "ave")
dend <- as.dendrogram(hc)
library(dendextend)
par(mfrow = c(1,2), mar = c(5,2,1,0))
dend <- dend %>%
color_branches(k = 3) %>%
set("branches_lwd", c(2,1,2)) %>%
set("branches_lty", c(1,2,1))
plot(dend)
dend <- color_labels(dend, k = 3)
# The same as:
# labels_colors(dend) <- get_leaves_branches_col(dend)
plot(dend)
Either way, you should always have a look at the set
function, for ideas on what can be done to your dendrogram (this saves the hassle of remembering all the different functions names).