ggdendro | Tools to extract dendrogram plot data for use with 'ggplot2 | Data Visualization library

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 massive dendrogram with hundreds of names on it, that I'd like to be make interactive so that users can draw a box and "zoom in" on the names and part of the tree of interest. The original code for creating it is borrowed from here. Pictured here:

I turned it into a shiny app and borrowed some code from here in order to make it zoomable. And it KINDA works. It runs, the two graphs show up, and nothing gives me an error. But it doesn't work as intended. (I'll post code below). What I mean is that if I were to simply render my plot outside of shiny, all the names and everything are included. But when it renders in shiny, I can't draw my box over the names, only the lines of the dendrogram (hope that makes sense), and the "zoomed" graph is turned sideways (something to do with the coord_cartesian? What would I use instead) and looks very weird when it "zooms". Lastly I can't see both graphs at the same time and have to use a scroll bar to get to them, pictured:

Help! Code below (its from an r markdown document if that matters, sorry I couldn't include the actual data, has real names.

I'm having trouble right aligning horizontal y axis titles for multiple plots in R ggplot2. I have a main plot which is a dendrogram with leaf labels created using the ggdendro package, and I have multiple color bars below the main plot with titles to the left. If I use grid.arrange to place the plots on the same page, I'm able to get good vertical spacing between the plots, but I'm not able to right-align the y axis titles for the color bars consistently. If I use plot_grid, I can right-align the y axis titles consistently, but I'm having trouble getting appropriate vertical spacing between plots. Any help would be appreciated!

Update: Two suggested solutions work equally well so I'm accepting the first one as the answer. Using ggarrange from the egg package and using plot_grid with align = "v" instead of align = "hv" both fixed my problem.

Create main plot and color bars:

I am trying to apply dendextend in order to color the ggdendro labels. I get this error:

How can I change the labels of the dendrogram to them matching name in the list? At the moment I only get the list number.

Code:

My task is to create a dendrogram, but the leaf nodes shows blunt edges. How would I extend the length of the leaf node, and add node labels?

Please see the current and expected images below.

Data: