To stupid to find good parameters for a pretty tree

[Tony Hei]

Hello!

I really like the idea of programming the trees. However, in the moment, I feel tremendously stupid since I cannot get ETE to do what I want. I try to format the newick tree in the attachment to something remotely similar as in the pdf.

First of all, I want to get rid of the "circles". If I use node["size"] = 0, all branches automatically get the length 0.
If I try to scale the branch length with TS.scale = 100 (I tried several orders of magnitude), The tree loses its height completely. ???

If I show the scale, instead of 0.2 or something, it computes 38000000. ?

It basically sums down to the fact, that I am unable to find the right values for the tree to look only remotely similar to what I want it to look like.

Can you provide me with a pointer to what I might change?

All the best!

Here is my code:

from ete2 import Tree, faces, AttrFace, TreeStyle, NodeStyle, TextFace
 

def treestyledef():
    TS = TreeStyle()
    TS.mode = "r" #rectangular
    TS.root_opening_factor = 0.75
    #TS.min_leaf_separation = 100 # pixels
    #TS.extra_branch_line_type = 0 # 0=solid, 1=dashed, 2=dotted
    TS.show_scale = True
    TS.show_leaf_name = False
    TS.scale = 38000000
    TS.optimal_scale_level = "mid"
    TS.show_leaf_name = False
    #TS.force_topology = True
    return TS
 
 
def nodestyledef(plant, PlantLib):
    node = NodeStyle()
    node["fgcolor"] = PlantLib[plant]
    node["shape"] = "circle"
    node["size"] = 1
    #node.opacity = 0
    node["vt_line_color"] = PlantLib[plant]
    node["hz_line_color"] = PlantLib[plant]
    node["vt_line_width"] = 0
    node["hz_line_width"] = 0
    node["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
    node["hz_line_type"] = 0
    return node
   
   
def PlantLibraryColors():

    PlantLib = {}

    PlantLib["Aco"] = "Red"
    PlantLib["Ara"] = "LightCoral"
    PlantLib["Brapa"] = "LightSalmon"  
    PlantLib["Bdist"] = "LimeGreen"
    PlantLib["Cpapa"] = "HotPink"
    PlantLib["Gmax"] = "DeepPink"
    PlantLib["Malus"] = "OrangeRed"
    PlantLib["Mimulus"] = "DarkOrange"
    PlantLib["Mtrun"] = "DarkKhaki"
    PlantLib["Osati"] = "SeaGreen"
    PlantLib["Ptrich"] = "BlueViolet"
    PlantLib["Slyco"] = "Purple"
    PlantLib["Sphureja"] = "Indigo"  
    PlantLib["Tcacao"] = "SaddleBrown"  
    PlantLib["Vvini"] = "DarkBlue"
    PlantLib["zm"] = "DarkGreen"
    PlantLib["Musa"] = "Lime"
    PlantLib["Pdacty"] = "LightGreen"
    PlantLib["Picabi"] = "DarkCyan"
    PlantLib["Ptaeda"] = "MediumAquamarine"
    PlantLib["Bvulg"] = "DarkRed"
    PlantLib["Taesti"] = "Olive"
    PlantLib["Turu"] = "OliveDrab"
   
    PlantLib["Dmel"] = "Black"  
    PlantLib["Drerio"] = "Black"
    PlantLib["hs"] = "Black"
    PlantLib["Mumu"] = "Black"
    PlantLib["Bmori"] = "Black"

    PlantLib["none"] = "Black"    
   
    return PlantLib

   
t = Tree("28plants_060id_LINERTs_MUSCLEcrop_example_tree.newick")
#t = Tree("28plants_060id_LINERTs_MUSCLEcrop_tree.newick")


PlantLib = PlantLibraryColors()


# Colors all nodes black
for node_p in t.traverse("postorder"):
    node = nodestyledef("none", PlantLib)
    node_p.img_style = node

   
# Colors the nodes according to plant species of the leaves
for key in PlantLib:
    node = nodestyledef(key, PlantLib)
    for node_p in t.traverse("postorder"):
   
    length = 0    
    for leaf in node_p.iter_leaves():
        length += 1
    count = 0
    for leaf in node_p.iter_leaves():
       
        if key in leaf.name:
        leaf.img_style = node
        count += 1
        if count == length:
            #node_p.set_style = node
            node_p.img_style = node
           
            name = leaf.name.strip("'").split('|')[0]
            font = TextFace(name)
            font.fgcolor = PlantLib[key]
            font.fsize = 6
            font.ftype = "Consolas"

TS = treestyledef()

t.show(tree_style=TS)
#t.render("mytree.png", w=600, tree_style=TS, units="dpi")

[Jaime Huerta Cepas]

Hi tony, the problem with branch lengths is due to the format of your newick tree. some symbols like ": ( [ ] ) " are not allowed to be part of node names (quotation marks have no effect). The parser is somehow reading part of the node name as the branch length. I have edited your file and replaces : by _, so now the tree looks nicer.

cheers,
J

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[Tony Hei]

Hello!

Wow! Thank you so much, this is awesome! I would have never guessed that this was the reason! I have been really frustrated, but now I can happily go to bed!

And thank you for the script, it works really well! I changed the part with the internal nodes as you have indicated and now it does exactly what I want it to do!

All the best,

Tony