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YuLab-SMU
tbl_tree object to phylo object lost bootstrap column
Dear author and users,
axmlng_phylo <- read.newick('concatenate_raxmlng_addoutgroup.raxml.support', node.label='support')
raxmlng_tibble <- as_tibble(raxmlng_phylo)
raxmlng_phylo_again < as.phylo(raxmlng_tibble )
raxmlng_phylo_tibble <- as_tibble(raxmlng_phylo_again)
the latter tibble lost the column bootstrap, how to avoid this?
Dropping the support column is the desired behaviour of as.phylo. This is because as.phylo returns a phylo object that cannot contain data. One way to fix this would be to join the tibbles.
@GuangchuangYu maybe you should add a way to get from a tibble to treedata
you can convert tbl_tree to treedata class, which contains phylo class and annotation data ..., using as.treedata, since tbl_tree contained support information. If you convert it to phylo class using as.phylo, it will not extract support or other annotation information, just return phylo class, because standard phylo class does not contain attributes to save annotation data information.
> library(treeio)
> library(tidytree)
> raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="treeio")
> tr <- read.raxml(raxml_file)
> tab1 <- as_tibble(tr)
> tr
'treedata' S4 object that stored information of
'/mnt/d/UbuntuApps/R/4.0.3/lib/R/library/treeio/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3'.
...@ phylo:
Phylogenetic tree with 64 tips and 62 internal nodes.
Tip labels:
A_Hokkaido_M1_2014_H3N2_2014, A_Czech_Republic_1_2014_H3N2_2014, FJ532080_A_California_09_2008_H3N2_2008, EU199359_A_Pennsylvania_05_2007_H3N2_2007, EU857080_A_Hong_Kong_CUHK69904_2006_H3N2_2006, EU857082_A_Hong_Kong_CUHK7047_2005_H3N2_2005, ...
Unrooted; includes branch lengths.
with the following features available:
'bootstrap'.
> tab1
# A tibble: 126 x 5
parent node branch.length label bootstrap
<int> <int> <dbl> <chr> <dbl>
1 66 1 0.00418 A_Hokkaido_M1_2014_H3N2_2014 NA
2 66 2 0.00239 A_Czech_Republic_1_2014_H3N2_2014 NA
3 74 3 0.00601 FJ532080_A_California_09_2008_H3N2_2008 NA
4 76 4 0.00594 EU199359_A_Pennsylvania_05_2007_H3N2_20… NA
5 77 5 0.00469 EU857080_A_Hong_Kong_CUHK69904_2006_H3N… NA
6 80 6 0.00234 EU857082_A_Hong_Kong_CUHK7047_2005_H3N2… NA
7 82 7 0.0000786 YGSIV1046_Sw_Binh_Duong_03_10_2010 NA
8 82 8 0.00111 YGSIV1044_Sw_Binh_Duong_03_08_2010 NA
9 85 9 0.00604 YGSIV1522_SW_HK_1071_2012 NA
10 85 10 0.00362 YGSIV1534_SW_HK_2454_2012 NA
# … with 116 more rows
> tr2 <- as.treedata(tab1)
> tr2
'treedata' S4 object'.
...@ phylo:
Phylogenetic tree with 64 tips and 62 internal nodes.
Tip labels:
A_Hokkaido_M1_2014_H3N2_2014, A_Czech_Republic_1_2014_H3N2_2014, FJ532080_A_California_09_2008_H3N2_2008, EU199359_A_Pennsylvania_05_2007_H3N2_2007, EU857080_A_Hong_Kong_CUHK69904_2006_H3N2_2006, EU857082_A_Hong_Kong_CUHK7047_2005_H3N2_2005, ...
Unrooted; includes branch lengths.
with the following features available:
'bootstrap'.
> as_tibble(tr2)
# A tibble: 126 x 5
parent node branch.length label bootstrap
<int> <int> <dbl> <chr> <dbl>
1 66 1 0.00418 A_Hokkaido_M1_2014_H3N2_2014 NA
2 66 2 0.00239 A_Czech_Republic_1_2014_H3N2_2014 NA
3 74 3 0.00601 FJ532080_A_California_09_2008_H3N2_2008 NA
4 76 4 0.00594 EU199359_A_Pennsylvania_05_2007_H3N2_20… NA
5 77 5 0.00469 EU857080_A_Hong_Kong_CUHK69904_2006_H3N… NA
6 80 6 0.00234 EU857082_A_Hong_Kong_CUHK7047_2005_H3N2… NA
7 82 7 0.0000786 YGSIV1046_Sw_Binh_Duong_03_10_2010 NA
8 82 8 0.00111 YGSIV1044_Sw_Binh_Duong_03_08_2010 NA
9 85 9 0.00604 YGSIV1522_SW_HK_1071_2012 NA
10 85 10 0.00362 YGSIV1534_SW_HK_2454_2012 NA
# … with 116 more rows
