when the string of metadata contains the character and numeric simultaneously in nhx format tree file. The related metadata will not be processed well.
Related Issue
96
Example
> library(ggtree)
ggtree v3.8.0 For help: https://yulab-smu.top/treedata-book/
If you use the ggtree package suite in published research, please cite
the appropriate paper(s):
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk 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
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
Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan
Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu. Ggtree: A serialized data
object for visualization of a phylogenetic tree and annotation data.
iMeta 2022, 1(4):e56. doi:10.1002/imt2.56
> library(ggplot2)
> library(treeio)
treeio v1.23.1 For help: https://yulab-smu.top/treedata-book/
If you use the ggtree package suite in published research, please cite
the appropriate paper(s):
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
Guangchuang Yu. Data Integration, Manipulation and Visualization of
Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
doi:10.1201/9781003279242
G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574
>
> treetext = "((((T0201:11.5[&&NHX],T0104:4.5[&&NHX]):1[&&NHX],
T0103:5.5[&&NHX]):0.5[&&NHX], T0106:3[&&NHX], T0107:2[&&NHX]):1[&&NHX],
T0102:7[&&NHX], (T0302:3[&&NHX],T0301:4[&&NHX]):1[&&NHX:S=GRIN2A Loss])[&&NHX];"
>
> tree <- read.nhx(textConnection(treetext))
> ggtree(tree, layout='ellipse') + geom_tiplab() +
geom_label(aes(x=branch, label=S), fill='lightgreen')
Description
when the string of metadata contains the character and numeric simultaneously in
nhxformat tree file. The related metadata will not be processed well.Related Issue
96
Example