Drawing lines between nodes of a phylogeny

[Bastien Boussau]

Hi, 

I'd like to draw lines to connect two nodes of a plotted tree. The idea behind this is to plot gene transfers along a species tree phylogeny. Ideally I would control the appearance of the line (thickness, transparency, color...). Even more ideally the lines could be curved, with an arrow at the end, for a nicer visualization.

Is there a way to do some version of this using ete3?

Thanks very much!

Bastien

[Luiz Thiberio Rangel]

Hi Bastien

    I made something similar using matplotlib itself, but hardcoded to a set of trees. What I can say is that it ended up too polluted. The solution I am using right now to highlight HGT is using nodeface and colormatching donnor/recipient.

    If you have too many transfer it is still a little harder to differentiate the different events but using the right colorscheme helps a lot.

thiberio,

[Bastien Boussau]

Hi Thiberio,

Thanks very much for your input. I would still like to try this line thing: indeed I can choose how many transfers I want to show so that it is not too cluttered. If you have some code/guidance on how to add lines to an ete3 plot, and how to get the coordinates of the nodes, or if you already have some code to do that, I would like to try!

Thanks again, 

Bastien 

[Jaime Huerta Cepas]

time ago a wrote some ad hoc code to draw things like in the screenshots attached. 

If useful, I think I could add it to core set to features of ETE 3. 

I will need to find a couple of days to work on it, but any feedback on what would you expect from a feature like this, might help

cheers, 

-jaime

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[Luiz Thiberio Rangel]

It looks like Jaime has it in a much better way than I did (as expected, =P). But when you render the tree it is returned a dict with the coordinates of each node, sorry but I don't have any code for that anymore.... =/

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L Thiberio Rangel

http://thiberio.ninja

[Jaime Huerta Cepas]

my code is still too crappy..., I would not really say I have anything at all yet :)

You approach is actually on the good track. Indeed, the dictionary returned by tree.render has the absolute coordinates of nodes, so you could easily hack something around that...

[Bastien Boussau]

Thanks very much Jaime and Thiberio, 

I think what you have in the figures you sent is quite nice and pretty close to what I had in mind (except that I would use it on a rooted/dated tree). I'd like to be able to draw lines between branches (e.g. between the middle of branches, but that could perhaps be controlled), not nodes, including ancestral branches, not just tips. Ideally I'd like to be able to control the width of the lines, their curvature, their color and their transparency, and possibly to place an arrowhead at one of the two ends. I know that's a lot to ask, so if that's not a feature you think would fit well within ete, I could also try to play around with the dictionary returned by tree.render.

Thanks very much again!

Bastien

[Luiz Thiberio Rangel]

Hey, Bastien,

if you don't really mind about using straight arrows it should be fairly easy. Take a look at this matplotlib example: http://matplotlib.org/examples/pylab_examples/arrow_simple_demo.html

You can easily control transparency, width, line and background color.

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[Bastien Boussau]

Thanks very much, but I have not been able yet to draw the tree, get the coordinates of the nodes, and plot something on top of it... 

I have not been able to understand the structure that tree.render returns... It does not seem to be a simple dictionary, is it?

Sorry I'm so slow!

Bastien

[Bastien Boussau]

Probably this last email was not very informative.

here is the type of things that I have tried, in a Jupyter notebook (which maybe is a problem...): 

t.render("%%inline", tree_style=ts) 

works and displays the tree.

I tried to store the output of render:

coord = t.render("%%inline", tree_style=ts)  

But then I don't know what to do with it... I have seen it is a IPython.core.display.Image, but calling imshow on it does not work. And I don't know how to get the coordinates of nodes out of coord...

Again, sorry I'm so slow, and thanks very much!

Bastien

[Jaime Huerta Cepas]

no problem. I am actually quite interested in having a proper way to visualize HGT events. I will try to add some generic code in the following weeks...  

[Bastien Boussau]

Great, thanks very much, please keep me posted when you're done!

[donova...@gmail.com]

Hello,

I would also be interested in being able to add custom visual elements (namely, lines) to an ETE rendering. Is there an example showing how a line can be drawn between two nodes, or two arbitrary points in a plot?

Cheers,
Donovan

[Jaime Huerta Cepas]

Hi Donovan, 

this is not support yet. At least not in a user friendly manner... 

There is some recent progress that I hope to integrate soon in the main branch. 

thanks. 

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[j.co...@gmail.com]

On Friday, December 11, 2015 at 11:56:01 AM UTC-5, Jaime wrote:
> time ago a wrote some ad hoc code to draw things like in the screenshots attached. 
> If useful, I think I could add it to core set to features of ETE 3. 
> I will need to find a couple of days to work on it, but any feedback on what would you expect from a feature like this, might help
>
>
> cheers, 
> -jaime
>

Jaime,
Is there a program to make visualizations like the ones you posted?
Thanks.

[Jaime Huerta Cepas]

there is only an open development branch trying to implement it: 

https://github.com/etetoolkit/ete/pull/247

cheers, 

-jaime

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