Visualize lineage tree using ggtree
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yun YAN ▴ 20
@yun-yan-6355
Last seen 5.3 years ago
Canada

I was wondering is it possible to visualize tree structure, in particular the branch nodes are shown.

 

The example is from wikipedia (https://en.wikipedia.org/wiki/Newick_format) and tree in the newick format is: (A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;

I can visualize tree by ggtree, but I did not know which parameters can highlight the branch nodes.

v <- '(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;'

ggtree(read.tree(text=v)) + geom_tiplab() 

 

My motivation of using ggtree is to visualize lineage tree, e.g. C.elegans, thus I care more about branching nodes (e.g. E and F in the example) and their child nodes.

@YGC

Thanks,

Yun

 

 

 

ggtree lineage • 2.5k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 days ago
China/Guangzhou/Southern Medical Univer…
root = 5
ggtree(read.tree(text=v)) + geom_point() + geom_text(aes(label=label), hjust=-.5) + geom_label2(aes(x=branch, label=branch.length, subset=(node != root))) -> p
rotate(p, root)

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Amazing ;-)

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 days ago
China/Guangzhou/Southern Medical Univer…
ggtree(read.tree(text=v)) + geom_point() + geom_text(aes(label=label), hjust=-.5)

the above code should work.

 

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v <- '((D,E)C,((((((((((((LONGGGGG,SHORT)LOVE, HATE)Y,Z)W,X)U,V)S,T)Q,R)O,P)L,M)I,J)H,K)F,G)B)A;'
ggtree(read.tree(text=v)) +
  # theme(plot.margin=unit(c(1,5,1.5,1.2),"cm")) +
  geom_point() +
  geom_text(aes(label=label), hjust=-.5)
plot(read.tree(text=v), show.node=TRUE, cex=.5)

 

The labels of end nodes are not displayed properly. Could you help me to set the correct parameter? I guess it might be `margin` but I still did not figure it out.

The default `plot` would not 'eat' the labels.

 

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