Suggestions for plotting options

[kingaa]

Suggestions for plotting options

[kingaa]

@mbutler808: some of these things are easily accommodated. Others require substantial thinking. On the whole, I'm wary of including all the options present in lower-level functions, because this becomes a headache to maintain. I agree that it is unfortunate that the ... is passed both to text and to plot. This is clearly a problem. I suppose one way to deal with it is to have ... passed, e.g., to plot and another option, say text_opts passed to text. There is also legend....

More generally, preparation of publication-quality figures need not be a goal of ouch, especially in the presence of other packages that have this as a goal. For example, I am very fond of ggtree, but I suppose there are others. The goal of ouch should be to support analysis using the models it provides. This does include a certain amount of graphics, so that users can e.g., load data and verify that it is entered correctly, paint a tree and check that it is done properly, visualize alternative hypotheses, etc. However, preparation of publication-quality graphics is something better left to other packages.

[kingaa]

Just pushed a new branch. Please have a look. Access to the options of the low-level functions plot, text, and legend is now possible. Ladderization is an option, with the default being to ladderize. The color palette is customizable.

[mbutler808]

Thank you so much Aaron. Really appreciate you working on this. I checked it out and marked a couple of things in new issues. I understand the pain in terms of maintenance, the publication-quality remark was just a bonus. Seems to me that this is very close to publication quality, and a lot of people would just go with this.

But the more important issue is plotting the trees and regimes for checking your data analysis. I should have indicated which was the biggest problem -- cutting off names. It has hindered us because we have a lot of unnamed species and long meta data. We used just short codes for a while, but finally had to check and there were errors that we missed because we couldnʻt see the names and/or sites. Itʻs an easy fix, I think, just need to calculate the space based on character length which I provided. This is really important for the analysis set-up and checking. Once everything is correct, of course we would make shorter names for publication.

Also one other comment - ouchʻs plotting routines are SO MUCH FASTER than ape or phylotools. Itʻs noticeable. So much more pleasant to do data exploration. My student is doing a biogeographic analysis on this huge phylogeny and needs to paint it in many different ways.

I have avoided ggplot and therefore ggtree, because ggplot is poorly documented and the syntax is so different. It was too frustrating to learn. But I may have to eventually.

Thanks,
Marguerite