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I have a tree with 18 tips that looks like this;

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 hoping someone can help me with the formating from phylo.to.plot() or suggest another method that can produce a similar output.

I have followed tutorial(s) here to produce an output but it seems difficult to alter the resulting figures.

Briefly these are my questions. I will expand further below.

1. How to plot a subregion of a "WorldHires" map, not entire region?
2. Change the shape of the points on the map, but maintain the colour?

Reproducible example:

Here is a very basic tree with some randomly assigned geographic locations

I have been trying to plot a tree with color-coded branches and tips using the ggtree package in R. Here is an example code using a tree of Anolis lizards.

I need to calculate the phylogenetic signal of more than 100 variables and store the results 'K stats' and 'p-value' to create a dataframe where I have 3 columns specifying variable names, K-stats, and p-value. I know how to do it for 1 variable but I just don't want to repeat that process 100 times. Also, I think a loop could be a more efficient way to do it avoiding problems.

So this is how I think it should go, I just don't know how to implement it. First, some dummy data:

cannot install phytools

tried with devtools

I am having a hard time trying to add several fossil tips to a 100 phylogenetic time trees.

Here is a drawing of what I want to do:

I would like to do it for my 100 trees contained in a single nexus file.

Thank you in advance.

EDIT:

Okay, I figured out how to do it. Here is the code for the example:

I try to measure the phylogenetic signal in two variables, a discrete and a continuous one. To do so, I use the δ-statistic (Borges et al 2018) and the K-statistic (Blomberg 2003), respectively. I have a tree, and two vectors corresponding to my variables. The line of code for these two statistics are the following:

1) delta(vector, tree, lambda0, se, sim, thin, burn)

2) phylosig(tree, vector, method = "K")

I get a single value each time. But I would like to randomize my vectors to test the significance of the orignal values. I would like to do 1000 repetitions and then proceed to a simple test of significance but, as I am a new R user, I have no idea how to do it. I think of something like this:

For δ: