1. G Yu. Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574

2. S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang*, X Bo*, G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. doi: 10.1093/molbev/msab166

3. G Yu^*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi: 10.1002/cpbi.96

4. 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. doi: 10.1093/molbev/msz240

5. 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. doi: 10.1093/molbev/msy194

6. 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. doi: 10.1111/2041-210X.12628

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Third, Intermediate color using gheatmap

Tucker Heptinstall