dendextend | Extending R 's Dendrogram Functionality | Build Tool library

I was able to create a stacked bar chart like this:

I'd like to create a hierarchical clustering tree of a relatively large dataset (>3000 obs). Unfortunately, by including so many labels at the terminal nodes, the tree looks very cluttered and contains lots of unnecessary information. So to reduce the clutter, I'd like to just label one observation of interest. I have removed all of the labels but I don't know how to retrieve and add the label that I'm interested in.

For this MWE, let's assume, I'd like to add the letter k to my dendrogram.

I am working with ecological data (the percentage abundance of different diatom species present at different depths in a sediment core) and want to plot the results alongside a dendrogram representing the results of a hierarchical cluster analysis (CONISS) that I will use to split the core into ecological zones.

This is an example of the type of thing I am trying to achieve:

I have successfully run the cluster analysis but am struggling to plot the dendrogram the way I would like to. Whenever I plot the dendrogram, it plots the leaves of the dendrogram in sequential order (as shown here). However, I need the leaves to plot by depth from the top of the sediment core so that there is a leaf present at each depth of the core that I have examined and so that there are gaps in the dendrogram where I have missing samples (as shown here). (Note there is no y-axis shown here as the dendrogram will join onto the rest of the diagram, which already contains the y-axis.)

I managed to create the latter plot through the rioja package using plot.chclust and providing the depths for the leaves to the xvar argument. However, I have constructed the rest of my diagram (the species abundance data, PCA results etc.) with ggplot (and the help of the tidypaleo package) and then combined the various aspects of it using cowplot. I need to be able to create the dendrogram through ggplot in order to add it to my main diagram. I have investigated both the ggdendro and dendextend packages but can't find a way to plot the dendrogram according to depth using these. Is this possible? Do these packages have a function to do this that I am not aware of? I started looking into the source code for these packages as well as for as.dendrogram to see if I could figure out a way of modifying the functions to plot the leaves by depth but it is beyond my skill level. I was wondering if anyone has a solution to enable me to plot my dendrogram by depth in my sediment core rather than in sequential order?

This is the data that I have used to calculate the distance matrix in the code below. (Apologies for the very long dput!)

I have a heatmap I made through R with pheatmap package :

The problem is that it's a bit unlisible ( I 've exported it on a pdf but we need to zoom to see the whole picture) plus I only want to keep the dendogram and tidy the y axis with the group column to have something like this :

Here is a look of my datas :

Upon opening a project on rstudio i have the following Warning:

I have the following code:

This is a similar question but not quite the same since I would like to do this with dendextend. My issue is that some of the names of my labels are quite long and I would like to just remove them. I had tried a few techniques already.

1. I tried changing cex = 0
2. I tried changing the color to white but all this does is hide the labels and when the names are long is still an issue.
3. I tried plotting labels =F , but this does not work as well. Is there anyway to completely eliminate the labels? Here is an example code.

I wish to visualize how well a clustering algorithm is doing (with certain distance metric). I have samples and their corresponding classes. To visualize, I cluster and I wish to color the branches of a dendrogram by the items in the cluster. The color will be the color most items in the hierarchical cluster correspond to (given by the data\classes).

Example: If my clustering algorithm chose indexes 1,21,24 to be a certain cluster (at a certain level) and I have a csv file containing a class number in each row corresponding to lets say 1,2,1. I want this edge to be coloured 1.

Example Code:

The following code produces the shown plot.