remove annoying node dots on branches

phylotastic / phylotastic-portal

Web tool (ruby on rails) providing access to phylotastic services for acquiring species trees.

https://github.com/phylotastic/phylotastic/wiki

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remove annoying node dots on branches #348

Open arlin opened 5 years ago

arlin commented 5 years ago

Screen Shot 2019-04-04 at 3 10 01 PM Trees are once again appearing with dots or squares for internal nodes with 1 child. Users do not expect this and do not know what it means. Therefore, it is confusing. Please remove it.

bomeara commented 5 years ago

Generally, having an option to return a tree without singleton nodes would be great -- it would fix the problem here, as well as for some of @jwiggi18's current work intended for displaying trees on EOL

abusalehmdtayeen commented 5 years ago

I have added the singleton node removal feature by default as @bomeara suggested. I think it is fixed now. @arlin can you please test your example again?

arlin commented 5 years ago

Thanks! Screen Shot 2019-04-06 at 9.17.33 AM.png

arlin commented 5 years ago

I'm seeing this problem again. I think that the problem was never fixed. I don't see a problem with the original tree, only with the scaled trees.

To reproduce the bug, here is what to do. Begin with this list

Equus caballus
Cervus canadensis
Sus scrofa
Balaenoptera acutorostrata
Balaena mysticetus
Orcinus orca
Platanista gangetica
Hippopotamus amphibius
Mirounga leonina
Hydrurga leptonyx
Phoca vitulina
Otaria byronia
Elephas maximus
Dugong dugon
Trichechus manatus
Ursus maritimus
Procyon lotor

Get the tree. Get the OT scaled tree. Add the 3 yellow boxes.

Now do the same thing, but use the Median scaled tree. the images below show both of them.

abusalehmdtayeen commented 5 years ago

@ducvan0212, I think the problem is happening because ete preserves the node actions between different calls. Since the tree is changed after scaling, sometimes the boxes remain in their old places. Can you please change the treeid every time scaling method is called. That would reset the actions and probably solve the problem.

ducvan0212 commented 5 years ago

@abusalehmdtayeen can you check if the issue still exists?

abusalehmdtayeen commented 5 years ago

I think the problem is fixed now. We clear the node actions when any scaling method is applied. So the user needs to reapply his actions for the new version of the tree.

abusalehmdtayeen commented 5 years ago

@arlin , if you are referring to the little misplaced dots, then we can't fix it. It is an internal issue of ETE.

arlin commented 5 years ago

is the fix on production yet? I tried it tonight and I still see the problem.

abusalehmdtayeen commented 5 years ago

@arlin , I think I have finally fixed the problem. Can you please check? I want to close this issue as soon as possible.