拆分数据帧，并根据特定列对拆分的值进行排序。

Question

我有下面的数据框架

tdf <- structure(list(GO = c("Cytokine-cytokine receptor interaction", 
"Cytokine-cytokine receptor interaction|Endocytosis", "I-kappaB kinase/NF-kappaB signaling", 
"NF-kappa B signaling pathway", "NF-kappaB import into nucleus", 
"T cell chemotaxis"), PosCount = c(17, 18, 4, 5, 1, 2), shortgo = structure(c(7L, 
7L, 18L, 18L, 18L, 21L), .Label = c("TNF", "adaptive", "alpha", 
"apop", "beta", "chemokine", "cytokine", "death", "defense", 
"gamma", "immune response", "infla", "interleukin-1 ", "interleukin-10 ", 
"interleukin-12 ", "interleukin-18 ", "interleukin-6 ", "kappa", 
"migration", "stress", "taxis", "wound"), class = "factor")), .Names = c("GO", 
"PosCount", "shortgo"), class = "data.frame", row.names = c(NA, 
6L))

看起来是这样的：

> tdf
                                                  GO PosCount  shortgo
1             Cytokine-cytokine receptor interaction       17 cytokine
2 Cytokine-cytokine receptor interaction|Endocytosis       18 cytokine
3                I-kappaB kinase/NF-kappaB signaling        4    kappa
4                       NF-kappa B signaling pathway        5    kappa
5                      NF-kappaB import into nucleus        1    kappa
6                                  T cell chemotaxis        2    taxis

我想要做的是根据shortgo拆分数据帧，然后按照PosCount对其GO成员进行排序，生成这个(手工构建的)：

$cytokine
[1] Cytokine-cytokine receptor interaction|Endocytosis
[2] Cytokine-cytokine receptor interaction 

$kappa
[1] NF-kappa B signaling pathway
[2] I-kappaB kinase/NF-kappaB signaling 
[3] NF-kappaB import into nucleus

$taxis
[1] T cell chemotaxis

我被困在这：

> split(tdf$GO,tdf$shortgo)
Error in split.default(tdf$GO, tdf$hsortgo) : 
  group length is 0 but data length > 0

我该怎么做呢？

Answer 1

在拆分之前，您可以先订购数据：

library(dplyr)
tdf <- tdf %>% group_by(shortgo) %>% arrange(desc(PosCount))

然后分开：

ldf <- split(tdf$GO, tdf$shortgo, drop=TRUE)

它提供所需的(有序)输出：

> ldf
$cytokine
[1] "Cytokine-cytokine receptor interaction|Endocytosis"
[2] "Cytokine-cytokine receptor interaction"            

$kappa
[1] "NF-kappa B signaling pathway"       
[2] "I-kappaB kinase/NF-kappaB signaling"
[3] "NF-kappaB import into nucleus"      

$taxis
[1] "T cell chemotaxis"

当您想要在数据文件列表中拆分数据文件时，可以使用：

ldf <- split(tdf, tdf$shortgo, drop=TRUE)

一个具有R(provided by @Henrik in the comments)基的解：

split(tdf$GO[order(tdf$shortgo, -tdf$PosCount)], tdf$shortgo, drop=TRUE)

Answer 2

使用data.table，您可以使用 to reorder your data.table by reference，然后按如下方式分组：

require(data.table)
ans = setorder(setDT(tdf), shortgo, -GO)[, .(GO_list = list(GO)), by=shortgo]

我建议将其保持为这样，因为对其执行计算更容易。但是，如果你坚持你的最终结构，那么你可以：

ans = setattr(ans$GO_list, 'names', as.character(ans$shortgo))

如果不希望通过引用重新排序原始数据，请执行以下操作：

ans = setDT(tdf)[order(shortgo, -GO), .(GO_list = list(GO)), by=shortgo]