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Added ggdensitree method #253

Merged
merged 1 commit into from
Sep 11, 2019
Merged

Added ggdensitree method #253

merged 1 commit into from
Sep 11, 2019

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brj1
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@brj1 brj1 commented Sep 10, 2019

I'm finally ready for a PR. I also merged all my commits into a single commit since the history was messy.

ggdensitree can plot lists of phylogenetic trees (or list of treedata) such that

  • tips are aligned in the y axis
  • tips can optionally (actually default) be aligned in the x axis
  • colouring of edges can be match to an aesthetic/scale

Node and tip labeling can only be done on the first tree in the list. It is slow with a large number of trees (> 100)

ggdensitree can plot lists of phylogenetic trees (or list of treedata) such that
  - tips are aligned in the y axis and
  - tips can optionally (actually default) be aligned in the x axis
  - colouring of edges can be match to an aesthetic/scale
Node and tip labelling can only be done on the first tree in the list
@brj1
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brj1 commented Sep 10, 2019

Do you think that it would be better to add this functionality to multiPhylo plotting?

@GuangchuangYu
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I think it should works for multiPhylo.

@GuangchuangYu GuangchuangYu merged commit 3002ff9 into YuLab-SMU:master Sep 11, 2019
@GuangchuangYu
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I have made some small modifications, mostly for satisfying R check.

And introduce the branch.length = "none" parameter to plot the tree using cladogram by default. Otherwise, it may generate very weird figure using example tree like:

set.seed(2019)
x = ape::rmtree(3, 10)

@GuangchuangYu
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thanks for the PR.

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2 participants