My apologies, I just noticed that the cumulative plot was already on the
page, I had misinterpreted what that plot meant.
Russell
On Sat, Oct 28, 2023 at 10:56 PM Russell Engelman
wrote:
> Dear Liam,
>
> This is great, almost exactly what I needed. I will have to get our tree
> out and see if
Dear Liam,
This is great, almost exactly what I needed. I will have to get our tree
out and see if I can get it to work in R.
One question, is it possible to do a cumulative tree like this (
https://proopnarine.files.wordpress.com/2018/11/evolfaunas.png)? This is a
good example of the graph I am
I like Will's suggestion. Unfortunately, /phytools::ltt.simmap/ method
in /phytools/ on CRAN does not support ultrametric trees.
I have updated it on GitHub & also posted a workflow to my blog that may
capture what Russell is going for (if I understand it correctly):
The output from Liam's function should be pretty useable for ggplot, too. I
think the function has a plot argument that you can just set to False.
On Sat, Oct 28, 2023, 6:37 PM Russell Engelman
wrote:
> It looks like what Liam wrote (specifically, the final figure in the post)
> is pretty close
It looks like what Liam wrote (specifically, the final figure in the post)
is pretty close to what I am looking for.
Emmanuel's suggestion of using ltt.plots.coords might also work, and it
might be easier to input that data into ggplot if I could find some way to
merge the various matrices.
You could also map your states (in this case, taxonomic groupings) onto
your tree, then make an ltt plot with phytools::ltt(). Liam has a great
blog post about it here:
http://blog.phytools.org/2022/08/lineage-through-time-plots-for.html.
Best,
Will
--
*William
Hi Russell,
There are several implementations of LTT plots among several packages, so the
details certainly differ depending on which one(s) you use.
Maybe you can use the ape function ltt.plot.coords() which returns a matrix
with 2 columns giving the number of lineages for each node time of
Dear R-Sig-Phylo,
I was wondering if there was any way to color-code a lineage-through-time
plot, to highlight the proportion of taxa at specific intervals that belong
to a particular clade. I.e., an LTT plot of tetrapod diversity through
time, and I want to highlight the number of lineages at
