[SOLVED] How do I save a phytools phenogram as an image?

How do I save a phytools phenogram as an image?

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.

phenogram(tree_sub, bio01, colors = cols, fsize = 0.8, ftype = "i",
          xlab = ("Relative Time"), ylab = "Mean Annual Temperature (°C)",
          spread.labels = TRUE, spread.cost = c(1, 0))

ggsave(filename = "../output/APCT_phenogram_5Nov2021.png", plot = last_plot(), 
       width = 25, height = 16, units = "cm", dpi = 300)

Using plot = last_plot() saves instead a previous non-phenogram tree I had plotted using ggtree. Assigning my phenogram to an object called "tree_plot" and then calling that in ggsave produces the error:

Error: $ operator is invalid for atomic vectors

This seems to be because when I assign the phenogram to an object, it is only saving the x and y coordinates of each species in the tree (i.e. not the tree topology, branch lengths, axis labels, colors, etc.) Similarly, using png() doesn't work — it just produces a dotplot of points with the x and y coordinates listed in tree_plot.

tree_plot <- phenogram(tree_sub, bio01, colors = cols, fsize = 0.8, ftype = "i",
             xlab = ("Relative Time"), ylab = "Mean Annual Temperature (°C)",
             spread.labels = TRUE, spread.cost = c(1, 0))

png(filename = "../output/APCT_phenogram_5Nov2021.png",  width = 25, 
    height = 16, units = "cm", res = 300)

plot(tree_plot)

dev.off()

Does anyone know what kind of object R understands my phenogram to be when it's displaying the graph (shown below), and how I can save that, short of physically clicking through the export menu in RStudio?

this is what the plot that I'm trying to save looks like

Solution

If anyone comes across this, I figured it out with help from Dr. Revell, the creator of phytools. It turns out, having worked almost exclusively in ggplot2, I do not really know how to use png() properly!

This is how it should go:

png(filename = "../output/APCT_phenogram_5Nov2021.png",  width = 25, 
    height = 16, units = "cm", res = 300)

phenogram(tree_sub, bio01, colors = cols, fsize = 0.8, ftype = "i",
          xlab = ("Relative Time"), ylab = "Mean Annual Temperature (°C)",
          spread.labels = TRUE, spread.cost = c(1, 0))

dev.off()

So make a sort of empty PNG, input all the info about it, then plot whatever you're trying to plot, and then turn off the graphics device.