> library(treeio)
treeio v1.25.1.002 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
G Yu. Data Integration, Manipulation and Visualization of Phylogenetic
Trees (1st ed.). Chapman and Hall/CRC. 2022. ISBN: 9781032233574
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
> example(drop.tip)
drp.tp> nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")
drp.tp> nhx <- read.nhx(nhxfile)
drp.tp> tr1 <- drop.tip(nhx, c("ADH2", "ADH1"))
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
drp.tp> tr2 <- keep.tip(nhx, c("ADH2", "ADH1"))
ℹ invalid tbl_tree object. Missing column: parent.
ℹ invalid tbl_tree object. Missing column: parent.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
>
After
> library(treeio)
treeio v1.25.1.002 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
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
> example(drop.tip)
drp.tp> nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")
drp.tp> nhx <- read.nhx(nhxfile)
drp.tp> tr1 <- drop.tip(nhx, c("ADH2", "ADH1"))
drp.tp> tr2 <- keep.tip(nhx, c("ADH2", "ADH1"))
>
Description
using
options(check.tbl_tree.verbose=FALSE)
to suppress the warning message of check whether is a tbl_tree.Related Issue
https://github.com/YuLab-SMU/tidytree/issues/40
Example
Before
After