add select,filter,mutate,left_join for treedata #19

xiangpin · 2021-08-20T13:02:05Z

add select, filter, mutate, left_join for treedata object.
introduce keep.td argument to control whether return treedata object in select, filter, mutate.
keep.td=FALSE is default that will return tbl_df in select.
and keep.td=TRUE is default that will return treedata in filter and mutate.
And these verbs will only process the associated data of tree.
add left_join to add the external associated data to treedata.

Examples

> library(treeio)
treeio v1.17.2  For help: https://yulab-smu.top/treedata-book/

If you use treeio in published research, please cite:

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

> library(tidytree)
> nwk <- '(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);'
> dat <- tibble(node=c(1, 2, 3, 4, 5), group=c("A", "A", "A", "B", "B"), test=c(10, 20, 30, 40, 50))
>
> tree <- read.tree(text=nwk) %>% treeio::as.treedata()
> tree@data <- dat
> tree
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test
   <int> <chr> <lgl> <chr> <dbl>
 1     1 A     TRUE  A        10
 2     2 B     TRUE  A        20
 3     3 C     TRUE  A        30
 4     4 D     TRUE  B        40
 5     5 E     TRUE  B        50
 6     6 F     TRUE  NA       NA
 7     7 G     TRUE  NA       NA
 8     8 H     TRUE  NA       NA
 9     9 I     TRUE  NA       NA
10    10 J     TRUE  NA       NA
# … with 15 more rows

select

> tree %>% select(group)
# A tibble: 25 x 1
   group
   <chr>
 1 A
 2 A
 3 A
 4 B
 5 B
 6 NA
 7 NA
 8 NA
 9 NA
10 NA
# … with 15 more rows
> tree %>% select(node, group) %>% filter(!is.na(group))
# A tibble: 5 x 2
   node group
  <int> <chr>
1     1 A
2     2 A
3     3 A
4     4 B
5     5 B
> tree %>% select(-group, keep.td=TRUE)
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'test'.

# The associated data tibble abstraction: 25 x 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip  test
   <int> <chr> <lgl> <dbl>
 1     1 A     TRUE     10
 2     2 B     TRUE     20
 3     3 C     TRUE     30
 4     4 D     TRUE     40
 5     5 E     TRUE     50
 6     6 F     TRUE     NA
 7     7 G     TRUE     NA
 8     8 H     TRUE     NA
 9     9 I     TRUE     NA
10    10 J     TRUE     NA
# … with 15 more rows

filter

> tree %>% filter(group=="A", keep.td=FALSE)
# A tibble: 3 x 5
   node label isTip group  test
  <int> <chr> <lgl> <chr> <dbl>
1     1 A     TRUE  A        10
2     2 B     TRUE  A        20
3     3 C     TRUE  A        30
> tree %>% filter(group=="A")
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test
   <int> <chr> <lgl> <chr> <dbl>
 1     1 A     TRUE  A        10
 2     2 B     TRUE  A        20
 3     3 C     TRUE  A        30
 4     4 D     TRUE  NA       NA
 5     5 E     TRUE  NA       NA
 6     6 F     TRUE  NA       NA
 7     7 G     TRUE  NA       NA
 8     8 H     TRUE  NA       NA
 9     9 I     TRUE  NA       NA
10    10 J     TRUE  NA       NA
# … with 15 more rows
> tree %>% filter(group=="A" & test>=20)
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test
   <int> <chr> <lgl> <chr> <dbl>
 1     1 A     TRUE  NA       NA
 2     2 B     TRUE  A        20
 3     3 C     TRUE  A        30
 4     4 D     TRUE  NA       NA
 5     5 E     TRUE  NA       NA
 6     6 F     TRUE  NA       NA
 7     7 G     TRUE  NA       NA
 8     8 H     TRUE  NA       NA
 9     9 I     TRUE  NA       NA
10    10 J     TRUE  NA       NA
# … with 15 more rows

mutate

> tree %>% mutate(type="A", keep.td=FALSE)
# A tibble: 25 x 6
    node label isTip group  test type
   <int> <chr> <lgl> <chr> <dbl> <chr>
 1     1 A     TRUE  A        10 A
 2     2 B     TRUE  A        20 A
 3     3 C     TRUE  A        30 A
 4     4 D     TRUE  B        40 A
 5     5 E     TRUE  B        50 A
 6     6 F     TRUE  NA       NA A
 7     7 G     TRUE  NA       NA A
 8     8 H     TRUE  NA       NA A
 9     9 I     TRUE  NA       NA A
10    10 J     TRUE  NA       NA A
# … with 15 more rows
> tree %>% mutate(test="A", keep.td=FALSE)
# A tibble: 25 x 5
    node label isTip group test
   <int> <chr> <lgl> <chr> <chr>
 1     1 A     TRUE  A     A
 2     2 B     TRUE  A     A
 3     3 C     TRUE  A     A
 4     4 D     TRUE  B     A
 5     5 E     TRUE  B     A
 6     6 F     TRUE  NA    A
 7     7 G     TRUE  NA    A
 8     8 H     TRUE  NA    A
 9     9 I     TRUE  NA    A
10    10 J     TRUE  NA    A
# … with 15 more rows
> tree %>% mutate(test="A")
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group test
   <int> <chr> <lgl> <chr> <chr>
 1     1 A     TRUE  A     A
 2     2 B     TRUE  A     A
 3     3 C     TRUE  A     A
 4     4 D     TRUE  B     A
 5     5 E     TRUE  B     A
 6     6 F     TRUE  NA    A
 7     7 G     TRUE  NA    A
 8     8 H     TRUE  NA    A
 9     9 I     TRUE  NA    A
10    10 J     TRUE  NA    A
# … with 15 more rows

left_join

> set.seed(123)
> df <- data.frame(label=tree@phylo$tip.label, value=abs(rnorm(length(tree@phylo$tip.label))))
> N <- tree %>% treeio::Nnode(internal.only=FALSE)
> dt <- data.frame(ind=rep(seq_len(N), 2), group=rep(c("A","B"), each=N))
> tr2 <- tree %>% left_join(df, by="label")
> tr3 <- tree %>% left_join(dt, by=c("node"="ind"))
> tr2
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test', 'value'.

# The associated data tibble abstraction: 25 x 6
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test  value
   <int> <chr> <lgl> <chr> <dbl>  <dbl>
 1     1 A     TRUE  A        10 0.560
 2     2 B     TRUE  A        20 0.230
 3     3 C     TRUE  A        30 1.56
 4     4 D     TRUE  B        40 0.0705
 5     5 E     TRUE  B        50 0.129
 6     6 F     TRUE  NA       NA 1.72
 7     7 G     TRUE  NA       NA 0.461
 8     8 H     TRUE  NA       NA 1.27
 9     9 I     TRUE  NA       NA 0.687
10    10 J     TRUE  NA       NA 0.446
# … with 15 more rows
> tr3
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test', 'group.y'.

# The associated data tibble abstraction: 25 x 6
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test group.y
   <int> <chr> <lgl> <chr> <dbl> <list>
 1     1 A     TRUE  A        10 <tibble [2 × 1]>
 2     2 B     TRUE  A        20 <tibble [2 × 1]>
 3     3 C     TRUE  A        30 <tibble [2 × 1]>
 4     4 D     TRUE  B        40 <tibble [2 × 1]>
 5     5 E     TRUE  B        50 <tibble [2 × 1]>
 6     6 F     TRUE  NA       NA <tibble [2 × 1]>
 7     7 G     TRUE  NA       NA <tibble [2 × 1]>
 8     8 H     TRUE  NA       NA <tibble [2 × 1]>
 9     9 I     TRUE  NA       NA <tibble [2 × 1]>
10    10 J     TRUE  NA       NA <tibble [2 × 1]>
# … with 15 more rows
> tr3 %>% left_join(dt, by=c("node"="ind"))
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        'group',        'test', 'group.y',      'group.y.y'.

# The associated data tibble abstraction: 25 x 7
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip group  test group.y          group.y.y
   <int> <chr> <lgl> <chr> <dbl> <list>           <list>
 1     1 A     TRUE  A        10 <tibble [2 × 1]> <tibble [2 × 1]>
 2     2 B     TRUE  A        20 <tibble [2 × 1]> <tibble [2 × 1]>
 3     3 C     TRUE  A        30 <tibble [2 × 1]> <tibble [2 × 1]>
 4     4 D     TRUE  B        40 <tibble [2 × 1]> <tibble [2 × 1]>
 5     5 E     TRUE  B        50 <tibble [2 × 1]> <tibble [2 × 1]>
 6     6 F     TRUE  NA       NA <tibble [2 × 1]> <tibble [2 × 1]>
 7     7 G     TRUE  NA       NA <tibble [2 × 1]> <tibble [2 × 1]>
 8     8 H     TRUE  NA       NA <tibble [2 × 1]> <tibble [2 × 1]>
 9     9 I     TRUE  NA       NA <tibble [2 × 1]> <tibble [2 × 1]>
10    10 J     TRUE  NA       NA <tibble [2 × 1]> <tibble [2 × 1]>
# … with 15 more rows
>

xiangpin · 2021-08-21T12:43:36Z

add unnest, pull, rename

pull

> library(tidytree)
> library(treeio)
treeio v1.17.2  For help: https://yulab-smu.top/treedata-book/

If you use treeio in published research, please cite:

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

> nwk <- '(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);'
> tr <- read.tree(textConnection(nwk))
> dat <- data.frame(label=rep(tr$tip.label, 2), value=abs(rnorm(length(tr$tip.label)*2)), group=rep(c("A", "B"), each=length(tr$tip.label)))
> dat
   label     value group
1      A 1.5519595     A
2      B 1.3769063     A
3      C 0.2054155     A
4      D 1.1060085     A
5      E 0.6554567     A
6      F 0.4969638     A
7      G 0.8210107     A
8      H 0.8286685     A
9      I 0.1559962     A
10     J 0.2080823     A
11     K 1.1358309     A
12     L 0.5969092     A
13     M 1.9534269     A
14     A 0.1723078     B
15     B 0.6882117     B
16     C 0.8640694     B
17     D 0.2769176     B
18     E 1.4081071     B
19     F 1.9001461     B
20     G 0.6673657     B
21     H 0.2133854     B
22     I 2.1669321     B
23     J 0.2632242     B
24     K 0.1254599     B
25     L 1.6644862     B
26     M 1.2938236     B
> tr %>% left_join(dat, by="label")
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        '',     'value',        'group'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip value            group
   <int> <chr> <lgl> <list>           <list>
 1     1 A     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 2     2 B     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 3     3 C     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 4     4 D     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 5     5 E     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 6     6 F     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 7     7 G     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 8     8 H     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 9     9 I     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
10    10 J     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
# … with 15 more rows
> tr %<>% left_join(dat, by="label")
> tr %>% pull(label, name=node)
  1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19  20
"A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M"  NA  NA  NA  NA  NA  NA  NA
 21  22  23  24  25
 NA  NA  NA  NA  NA

rename

> tr %>% rename(G=group)
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
        '',     'value',        'G'.

# The associated data tibble abstraction: 25 x 5
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip value            G
   <int> <chr> <lgl> <list>           <list>
 1     1 A     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 2     2 B     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 3     3 C     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 4     4 D     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 5     5 E     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 6     6 F     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 7     7 G     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 8     8 H     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
 9     9 I     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
10    10 J     TRUE  <tibble [2 × 1]> <tibble [2 × 1]>
# … with 15 more rows

unnest

> tr %>% unnest(cols=c(value, group))
# A tbl_df is returned for independent data analysis.
# A tibble: 38 x 5
    node label isTip value group
   <int> <chr> <lgl> <dbl> <chr>
 1     1 A     TRUE  1.55  A
 2     1 A     TRUE  0.172 B
 3     2 B     TRUE  1.38  A
 4     2 B     TRUE  0.688 B
 5     3 C     TRUE  0.205 A
 6     3 C     TRUE  0.864 B
 7     4 D     TRUE  1.11  A
 8     4 D     TRUE  0.277 B
 9     5 E     TRUE  0.655 A
10     5 E     TRUE  1.41  B
# … with 28 more rows

xiangpin added 7 commits August 20, 2021 20:38

update show

f10cc85

add AAbin class for tip_seq and anc_seq slot

07749f1

add filter, select, mutate for treedata object

a56153e

add left_join for treedata

8d5c6b6

add unnest for treedata

270a0a4

add pull for treedata

4edab3d

add rename for tredata

22a64e3

GuangchuangYu merged commit 652adbe into YuLab-SMU:master Aug 22, 2021

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add select,filter,mutate,left_join for treedata #19

add select,filter,mutate,left_join for treedata #19

xiangpin commented Aug 20, 2021

xiangpin commented Aug 21, 2021

add select,filter,mutate,left_join for treedata #19

add select,filter,mutate,left_join for treedata #19

Conversation

xiangpin commented Aug 20, 2021

select

filter

mutate

left_join

xiangpin commented Aug 21, 2021

pull

rename

unnest