如何在R中将列表列表转换为整洁的小标题或data.frame

Question

我有以下列表列表：

my_lol <- structure(list(coolfactor_score = list(structure(c(0.164477631065473, 
0.198253819406019, 0.396414447052519, 0.133118603987442, 0.107735498488546
), .Names = c("B", "Mac", "NK", "Neu", "Stro")), structure(c(0.186215537135912, 
0.18408529174803, 0.375349920115798, 0.247664923324821, 0.006684327675438
), .Names = c("B", "Mac", "NK", "Neu", "Stro"))), sr_crt = list(
    structure(list(crt = 0.133118603987442, sr = 0.407076876403305), .Names = c("crt", 
    "sr")), structure(list(crt = 0.18408529174803, sr = 0.0829181742326453), .Names = c("crt", 
    "sr"))), sample_names = c("Sample1", "Sample2")), .Names = c("coolfactor_score", 
"sr_crt", "sample_names"))

看起来像这样：

> my_lol
$coolfactor_score
$coolfactor_score[[1]]
        B       Mac        NK       Neu      Stro 
0.1644776 0.1982538 0.3964144 0.1331186 0.1077355 

$coolfactor_score[[2]]
          B         Mac          NK         Neu        Stro 
0.186215537 0.184085292 0.375349920 0.247664923 0.006684328 


$sr_crt
$sr_crt[[1]]
$sr_crt[[1]]$crt
[1] 0.1331186

$sr_crt[[1]]$sr
[1] 0.4070769


$sr_crt[[2]]
$sr_crt[[2]]$crt
[1] 0.1840853

$sr_crt[[2]]$sr
[1] 0.08291817



$sample_names
[1] "Sample1" "Sample2"
# Note that the number of samples can be more than 2 and cell type more than 5.

我如何将其整理到此数据框中（小标题）

CellType    Sample    CoolFactorScore  SR            CRT
B           Sample1   0.1644776        0.4070769     0.1331186
Mac         Sample1   0.1982538        0.4070769     0.1331186
NK          Sample1   0.3964144        0.4070769     0.1331186
Neu         Sample1   0.1331186        0.4070769     0.1331186
Stro        Sample1   0.1077355        0.4070769     0.1331186
B           Sample2   0.186215537      0.08291817    0.1840853
Mac         Sample2   0.184085292      0.08291817    0.1840853
NK          Sample2   0.375349920      0.08291817    0.1840853
Neu         Sample2   0.247664923      0.08291817    0.1840853
Stro        Sample2   0.006684328      0.08291817    0.1840853

Answer 1

一种使用基数R的方法：

mylist <- lapply(1:2, function(i) {
  #this is the important bit where you extract the corresponding elements
  #of sample 1 first and sample 2 second.
  df <- data.frame(lapply(my_lol, '[', i))
  names(df) <- c('CoolFactorScore', 'CRT', 'SR', 'Sample')
  df$CellType <- rownames(df)
  row.names(df) <- NULL
  df
})

do.call(rbind, mylist)

日期：

  CoolFactorScore       CRT         SR  Sample CellType
1      0.164477631 0.1331186 0.40707688 Sample1        B
2      0.198253819 0.1331186 0.40707688 Sample1      Mac
3      0.396414447 0.1331186 0.40707688 Sample1       NK
4      0.133118604 0.1331186 0.40707688 Sample1      Neu
5      0.107735498 0.1331186 0.40707688 Sample1     Stro
6      0.186215537 0.1840853 0.08291817 Sample2        B
7      0.184085292 0.1840853 0.08291817 Sample2      Mac
8      0.375349920 0.1840853 0.08291817 Sample2       NK
9      0.247664923 0.1840853 0.08291817 Sample2      Neu
10     0.006684328 0.1840853 0.08291817 Sample2     Stro

Answer 2

这不是一个很优雅的方法：

int <- lapply(1:2, function(x) do.call(data.frame, 
              c(list(CoolFactorScore=my_lol[[1]][[x]]), 
                my_lol[[2]][[x]], 
                list(Sample=my_lol[[3]][[x]])))) 
do.call(rbind, int)

      CoolFactorScore       crt         sr  Sample
B         0.164477631 0.1331186 0.40707688 Sample1
Mac       0.198253819 0.1331186 0.40707688 Sample1
NK        0.396414447 0.1331186 0.40707688 Sample1
Neu       0.133118604 0.1331186 0.40707688 Sample1
Stro      0.107735498 0.1331186 0.40707688 Sample1
B1        0.186215537 0.1840853 0.08291817 Sample2
Mac1      0.184085292 0.1840853 0.08291817 Sample2
NK1       0.375349920 0.1840853 0.08291817 Sample2
Neu1      0.247664923 0.1840853 0.08291817 Sample2
Stro1     0.006684328 0.1840853 0.08291817 Sample2

Answer 3

这是使用data.table包功能的无循环解决方案。

library(data.table)

步骤1：解开清单

unlist(my_lol) -> tmp1

步骤2：转置并将其转换为data.table
这样，您将获得可以由原始数据组成的最大表格。 应该根据要求将其转换为长表（在进一步的步骤中）。

as.data.table(t(tmp1)) -> tmp2

步骤3：需要将“ sample_names1”和“ sample_names2”手动转换为“ Sample”。
如果要泛化为多个sample_names值，则应根据可能值的语法修改此步骤。 （此版本适用于以下sample_names值语法：'Sample1'，'Sample2'，'Sample3'等。）

names(tmp2) <- gsub('sample_names\\d+', 'Sample', names(tmp2))

步骤4：基于tmp2表的字段名称创建度量字段名称

measure <- unique(names(tmp2))

步骤5：从宽表（tmp2）创建更长的表（tmp3）

tmp3 <- melt(tmp2, 
             measure.vars = patterns(measure), 
             value.name = measure)

第6步：根据请求重命名列

names(tmp3) <- gsub('coolfactor_score.', '', names(tmp3))
names(tmp3) <- gsub('sr_crt.', '', names(tmp3))
setnames(tmp3, 'crt', 'CRT')
setnames(tmp3, 'sr', 'SR')

步骤7：从tmp3创建更长的表（mylist）

mylist <- melt(tmp3,
               id.vars = c('Sample',
                           'CRT',
                           'SR'),
               measure.vars = c('B', 
                                'Mac',  
                                'NK',   
                                'Neu',
                                'Stro'),
               value.name = 'CoolFactorScore',
               variable.name = 'CellType')

步骤8：根据要求对列进行重新排序

setcolorder(mylist, c('CellType', 'Sample', 'CoolFactorScore', 'SR', 'CRT'))

步骤9：根据要求对行重新排序

mylist <- mylist[order(Sample, CellType)]