read.treeqza

read.treeqza

Usage

read.treeqza(treeqza, node.label = "label", ...)

Arguments

treeqza

the qiime2 output file contained tree file.

node.label

parse node label as 'label' or 'support' value.

...

additional parameter, passed to 'read.tree'.

Value

phylo tree object or treedata object when node.label was parsed 'support'.

Examples

qzafile1 <- system.file("extdata/qiime2treeqza", "fasttree-tree.qza", package="treeio")
qzafile2 <- system.file("extdata/qiime2treeqza", "iqt-tree.qza", package="treeio")
qzafile3 <- system.file("extdata/qiime2treeqza", "raxml-cat-tree.qza", package="treeio")
tr1 <- read.treeqza(qzafile1)
tr1
#> 
#> Phylogenetic tree with 20 tips and 18 internal nodes.
#> 
#> Tip labels:
#>   '682e91d7e510ab134d0625234ad224f647c14eb0', '206656bec2abdbc4aee37a661ef5f4a62b5dd6ae', 'b31aa3f04bc9d5e2498d45cf1983dfaf09faa258', '606c23e79bb730ad74e3c6efd72004c36674c17a', '0469f8d819bd45c7638d1c8b0895270a05f34267', '5525fb6dab7b6577960147574465990c6df070ad', ...
#> Node labels:
#>   , 0.765, 0.000, 0.554, 0.926, 0.917, ...
#> 
#> Unrooted; includes branch lengths.
tr2 <- read.treeqza(qzafile2)
tr2
#> 
#> Phylogenetic tree with 20 tips and 18 internal nodes.
#> 
#> Tip labels:
#>   e84fcf85a6a4065231dcf343bb862f1cb32abae6, 5525fb6dab7b6577960147574465990c6df070ad, d162ed685007f5adede58f14aece31dfa1b60c18, 0469f8d819bd45c7638d1c8b0895270a05f34267, 8a1c44eb462ed58b21f3fdd72dd22bb657db2980, 606c23e79bb730ad74e3c6efd72004c36674c17a, ...
#> 
#> Unrooted; includes branch lengths.
tr3 <- read.treeqza(qzafile3)
tr3
#> 
#> Phylogenetic tree with 20 tips and 18 internal nodes.
#> 
#> Tip labels:
#>   ed1acad8a98e8579a44370733533ad7d3fed8006, 9b220cae8d375ea38b8b481cb95949cda8722fcb, 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8, 2e3b2c075901640c4de739473f9246385430b1ed, 682e91d7e510ab134d0625234ad224f647c14eb0, d44b129a6181f052198bda3813f0802a91612441, ...
#> 
#> Rooted; includes branch lengths.
# parse node label as 'support' value.
qzafile4 <- system.file("extdata/qiime2treeqza", "raxml-cat-bootstrap-tree.qza", package="treeio")
tr4 <- read.treeqza(qzafile4, node.label="support")
tr4
#> 'treedata' S4 object'.
#> 
#> ...@ phylo:
#> 
#> Phylogenetic tree with 20 tips and 18 internal nodes.
#> 
#> Tip labels:
#>   d44b129a6181f052198bda3813f0802a91612441,
#> aa4698d2e2b1fa71d08e2934a923aad7374a18f6,
#> 6a36152105590b1eb095b9503e8f1f226fc73e43,
#> 418f1d469f08c99976b313028cf6d3f18f61dd55,
#> 9b220cae8d375ea38b8b481cb95949cda8722fcb,
#> 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8, ...
#> 
#> Unrooted; includes branch lengths.
#> 
#> with the following features available:
#>   'support'.
#> 
#> # The associated data tibble abstraction: 38 × 4
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#>     node label                                    isTip support
#>    <int> <chr>                                    <lgl>   <dbl>
#>  1     1 d44b129a6181f052198bda3813f0802a91612441 TRUE       NA
#>  2     2 aa4698d2e2b1fa71d08e2934a923aad7374a18f6 TRUE       NA
#>  3     3 6a36152105590b1eb095b9503e8f1f226fc73e43 TRUE       NA
#>  4     4 418f1d469f08c99976b313028cf6d3f18f61dd55 TRUE       NA
#>  5     5 9b220cae8d375ea38b8b481cb95949cda8722fcb TRUE       NA
#>  6     6 5aba6bd9debc23ded7041ffdcfe5d68a427e8ce8 TRUE       NA
#>  7     7 2e3b2c075901640c4de739473f9246385430b1ed TRUE       NA
#>  8     8 206656bec2abdbc4aee37a661ef5f4a62b5dd6ae TRUE       NA
#>  9     9 b31aa3f04bc9d5e2498d45cf1983dfaf09faa258 TRUE       NA
#> 10    10 606c23e79bb730ad74e3c6efd72004c36674c17a TRUE       NA
#> # ℹ 28 more rows