question about the MRCA
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biohellen
Jun 16, 2019, 10:56:45 PM6/16/19
to ggtree
Hi,
I library the pkg tidytree and ggtree, but still have the following MRCA error, could you please give me a hand?
> library(tidytree)
> library(ggtree)
> set.seed(1234)
> tree<-rtree(n=10)
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
> MRCA(tree,'t1','t7')
Error in UseMethod("MRCA") :
no applicable method for 'MRCA' applied to an object of class "phylo"
Looking forward to your reply
biohellen
Jun 16, 2019, 11:22:14 PM6/16/19
to ggtree
When I run the same code second time, the error changed, I've no idea about this problem, any help would be appreciated.
> library(ggtree)
> library(tidytree)
> set.seed(1234)
> tree<-rtree(n=10)
> MRCA(tree,'t1','t7')
Error in MRCA(tree, "t1", "t7") : unused argument ("t7")
在 2019年6月17日星期一 UTC+8上午10:56:45，biohellen写道：
Yu, Guangchuang
Jun 17, 2019, 4:51:07 AM6/17/19
to biohellen, ggtree
pls load treeio either.
--
1. 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
2. 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
3. Book: https://yulab-smu.github.io/treedata-book/
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--
--~--~---------~--~----~------------~-------~--~----~
Guangchuang Yu PhD
Professor
School of Basic Medical Sciences
School of Basic Medical Sciences
Southern Medical University
Guangzhou, China
-~----------~----~----~----~------~----~------~--~---
biohellen
Jun 17, 2019, 5:08:07 AM6/17/19
to ggtree
Hi Guangchuang,
The error is still:
> library(ggtree)
> library(tidytree)
> library(treeio)
> set.seed(1234)
> tree<-rtree(n=10)
> MRCA(tree,'t1','t7')
Error in MRCA(tree, "t1", "t7") : unused argument ("t7")
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
在 2019年6月17日星期一 UTC+8上午10:56:45，biohellen写道：
Hi,
Yu, Guangchuang
Jun 17, 2019, 6:59:42 AM6/17/19
to biohellen, ggtree
pls make sure you are using the latest release.
--
1. 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
2. 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
3. Book: https://yulab-smu.github.io/treedata-book/
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biohellen
Jun 17, 2019, 9:56:30 PM6/17/19
to ggtree
I think they should be the latest version:
> packageVersion("ggtree")
[1] ‘1.16.1’
> packageVersion("tidytree")
[1] ‘0.2.4’
> packageVersion("treeio")
[1] ‘1.8.1’
> set.seed(1234)
> tree<-rtree(n=10)
> MRCA(tree,'t1','t7')
Error in MRCA(tree, "t1", "t7") : unused argument ("t7")
Found more than one class "phylo" in cache; using the first, from namespace 'treeio'
Also defined by ‘tidytree’
在 2019年6月17日星期一 UTC+8上午10:56:45，biohellen写道：
Hi,
Yu, Guangchuang
Jun 18, 2019, 5:06:51 AM6/18/19
to biohellen, ggtree
```> packageVersion(“ggtree”)
[1] ‘1.16.1’
packageVersion(“treeio”)
[1] ‘1.8.1’
packageVersion(“tidytree”)
[1] ‘0.2.4’
set.seed(1234)
require(tidytree); require(treeio); require(ggtree)
tree = rtree(10)
MRCA(tree, ‘t1’, ‘t7’)
[1] 11
```
Did you restart R session after upgrading the pkgs? Otherwise I have no idea.
--
1. 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
2. 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
3. Book: https://yulab-smu.github.io/treedata-book/
---
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