将（征税）分类法数据的嵌套列表转换为数据框

Question

我有一些生物（微生物组）数据，其中有一堆 OTU，它们的名称在属和门级别之间的分类学分辨率各不相同。我正在尝试获得一个 table 所有比我给出的名称更低级别的分类法。

 testnames <- c("Prevotella", "Bacteroides", "Enterobacteriaceae")

我发现 taxize 是一个有用的包，可以提取我正在寻找的信息。

library("taxize")
reclass <- classification(testnames, db = 'ncbi')

这给我一个数据框列表

看起来像这样：

并且可以这样输入到R中：

structure(list(Prevotella = structure(list(name = c("cellular organisms", 
"Bacteria", "FCB group", "Bacteroidetes/Chlorobi group", "Bacteroidetes", 
"Bacteroidia", "Bacteroidales", "Prevotellaceae", "Prevotella"
), rank = c("no rank", "superkingdom", "no rank", "no rank", 
"phylum", "class", "order", "family", "genus"), id = c("131567", 
"2", "1783270", "68336", "976", "200643", "171549", "171552", 
"838")), .Names = c("name", "rank", "id"), row.names = c(NA, 
-9L), class = "data.frame"), Bacteroides = structure(list(name = c("cellular organisms", 
"Bacteria", "FCB group", "Bacteroidetes/Chlorobi group", "Bacteroidetes", 
"Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Bacteroides"
), rank = c("no rank", "superkingdom", "no rank", "no rank", 
"phylum", "class", "order", "family", "genus"), id = c("131567", 
"2", "1783270", "68336", "976", "200643", "171549", "815", "816"
)), .Names = c("name", "rank", "id"), row.names = c(NA, -9L), class = "data.frame"), 
    Enterobacteriaceae = structure(list(name = c("cellular organisms", 
    "Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", 
    "Enterobacteriaceae"), rank = c("no rank", "superkingdom", 
    "phylum", "class", "order", "family"), id = c("131567", "2", 
    "1224", "1236", "91347", "543")), .Names = c("name", "rank", 
    "id"), row.names = c(NA, -6L), class = "data.frame")), .Names = c("Prevotella", 
"Bacteroides", "Enterobacteriaceae"))

我真的很想把东西变成一个数据框，我可以将它作为分类法导入到 phyloseq 中 table。例如。看起来像的东西：

name Phylum Class Order Family Genus

Prevotella Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella

Bacteroides Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides

Enterobacteriaceae Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae

当然，一种方法是创建一个循环，遍历列表的每个元素，找到调用的变量 phylum，然后将其放入新的数据框中。也就是说，我觉得应该有一种更快的方法来应用这种转换，使用 plyr 或 dplyr 之类的东西。

我看到了一些看起来很接近的东西：

Converting nested list to dataframe

但他们似乎假设不想保存的数据较少，并且每个元素的数据帧大小均匀。有什么建议吗？

Answer 1

使用 dplyr 和 tidyr:

library(dplyr)
library(tidyr)

tibble(names = names(list), list) %>% 
  unnest() %>% 
  filter(rank %in% c("phylum","class","order","family","genus")) %>% 
  select(-id) %>% 
  spread(rank, name) %>% 
  select(name = names, phylum, class, order, family, genus)

# A tibble: 3 × 6
                name         phylum               class            order             family       genus
*              <chr>          <chr>               <chr>            <chr>              <chr>       <chr>
1        Bacteroides  Bacteroidetes         Bacteroidia    Bacteroidales     Bacteroidaceae Bacteroides
2 Enterobacteriaceae Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae        <NA>
3         Prevotella  Bacteroidetes         Bacteroidia    Bacteroidales     Prevotellaceae  Prevotella

这是做什么的：

使用列表名称和每个嵌套列表创建 tibble
取消列表嵌套
在排名列中过滤您想要的值
去掉 id 列
将排名行分散到列中，并填充名称中的值
Select你想要的顺序，将names重命名为name。

将（征税）分类法数据的嵌套列表转换为数据框

Turn a nested list of (taxize) taxonomy data into a data frame

r

plyr

dplyr