tree$tip.label in plot order??

[William Pearson]

As wonderful as ggtree() is, I have run into some limitations in combining different plot types using either geom_fruit() or facet_plot().

My solution is to simply combine the tree with a separate ggplot() panel using plot_grid().

But to do this correctly, I must order the taxa on the plot the same way they are ordered in the tree.  How can I find the order of the taxa in the tree so that I can use this order in a ggplot()?

Thanks,  Bill Pearson

[Yu, Guangchuang]

the answer was documented in the online book, see http://yulab-smu.top/treedata-book/chapter12.html#tiporder

I would recommend the aplot package for this purpose.

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1. G Yu*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. https://doi.org/10.1002/cpbi.96
2. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. http://dx.doi.org/10.1093/molbev/msz240
3. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194
4. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628
5. Book: https://yulab-smu.top/treedata-book/
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Guangchuang Yu PhD

Professor, Associate director

Department of Bioinformatics
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://yulab-smu.top

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