clade | Simple taxonomy management tool and document classifier

I'd like to place this data onto a bar plot using ggplot2

where the column "Clades" would be placed on the X axis and the values from each column (such as the values of 19A, for example) would be place on Y axis

I'm trying something like this:

I have one phylogenetic tree as picture below.

I did make a fake dataframe to get the legend, and now I would like to insert that legend to the center of phylogenetic tree. I used grid.arrange but I could not move the legend position.

The fake legend that I created

Here is the .tsv file for the following script.

Source code:

I'm describing my problem below:

Data Frame:

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

Is there a way to name the column of a tibble using a variable? I want to name the first column below Clade for example. I tried paste() and assign(), but neither function seems to do what I want.

This might be very straightforward but I am having bit of trouble while deleting unwanted line in my text file:

I am currently trying to plot a point graph using ggplot2. The data is of 3 categories, but for each of the categories, there are some selected points I would like to highlight (or make them show differently in the graph). There is no any special characteristics like what I manage to check on the previous examples (eg. last point of the category, point outside range,....).

Attached is the general view of the graph I have got currently, where each category was represented by default shapes.

The struggle is, how can I highlight the selected point on the graph, with the same shape used for each of the categories, but with different colors? So each of the point will be the same, just that the selected points are with colors other than black. I have 15 selected points for each of the categories to plot on.

Is this possible to do with ggplot2?

I cannot reach any case similar with mine, but instead some previous examples on manually assigning colors on the plot. I was just trying out to plot the categories with different colors instead of shapes, and use scale_fill_manual to plot the points in 2 different colors (base color and color for selected points), but it doesn't work, 6 colors appeared instead.

When I run a command (COMMAND) on one line of my input file (input.txt) I get an associated result where only one line is interesting, always starting by the world phylum.

For instance: