ggtree | : christmas_tree : Visualization and annotation | Data Visualization library

I need to plot a nice tree for a project. The problem is that I have to use a specific function to create the tree that creates a tree datatype and all the functions used to plot trees in a nice way (ggtree, rpart.plot) require other types of object. Could you please help me to change the object data type of the tree or suggest me other functions to plot them? I have to plot prune.result. I cannot use other functions to create and prune the tree. (I know I can use the simply plot function but I use the ggplot package in all the project so I would like something similar to that).

Thank you in advance

Given a tree with tip labels colored by a group eg:

I'm using the phenogram() function in the R package phytools to plot a phylogeny along axes of relative time (x) and phenotype, in this case mean annual temperature (y). It shows up in the plot window, but it doesn't seem to exist as a plot object that I can save externally as an image with ggsave.

Here is the main code and plot. I can provide a minimum reproducible example if necessary, but it's a lot of code, so I'm hoping this is perhaps a very easy and obvious thing to fix.

I am working with DNA sequence data in fasta files, and have to work only in R for this project. I do some manipulations using the seqinr package (selecting a subset of sequences, altering the fasta headers etc). For the next stage in the analysis I want to do a multiple sequence alignment, and have used the msa R package. I can get msa working if I import a fasta file, but I'm struggling to move directly within R from the seqinr list object to the Biostrings DNAStringSet object that I have used as input for msa.

Example data - Assume that fasta_file.fasta is a fasta file with contents as follows:

I am trying to visualize my ggtree and I seem to be stuck on the last final step; repositioning the tree labels from horizontal to verticle so that they do not overlap. If I change the geom = "text" on the geom_tiplab function, I get what I want but my labels are no longer coloured. Datasets here and here

Here is the code for reproducibility; Please help

I have data such as:

I would like to set x axis on a heatmap ggtree.

This is my code

I have a phylogenetic tree made by a Newick file.

I have been trying to use the ifelse function (similar to ternary operators in other languages) in R to evaluate an expression that if done correctly, will save me the need to generate many if/else statements. My code is below: