Несколько таблиц данных на одном листе с некоторым перекрытием имен и разделением заголовков столбцов

Question

У меня есть набор данных с несколькими таблицами в одном листе Excel, который я хотел бы объединить. Данные листа форматируются следующим образом:

group_no      group     variable       marker1     marker2     marker3
1             GR-01-1   1              -           -           A
1             GR-01-1   2              B           A           B
1             GR-01-1   3              A           B           -
1             GR-01-1   4              -           -           -
1             GR-01-1   5              B           -           B
group_no.     group     variable       marker 4    marker5     marker6    marker7
2             GR-01-1a  1              B           -           A          -
2             GR-01-1a  2              B           A           -          B
2             GR-01-1a  3              A           B           -          B
2             GR-01-1a  4              A           A           A          A
group_no      group     variable       marker8
3             GR-01-2   1              B
3             GR-01-2   2              A
3             GR-01-2   3              -
group_no      group     variable       marker9     marker10
4             GR-02-1   1              B           A
4             GR-02-1   2              A           A
4             GR-02-1   3              -           B
4             GR-02-1   4              B           B
4             GR-02-1   5              A           B
4             GR-02-1   6              -           A
group_no      group     variable       marker11    marker12    marker13
5             GR-02-2   d              B           B           A
5             GR-02-2   e              A           B           B
5             GR-02-2   f              B           -           -
5             GR-02-2   g              -           B           -

Как видно выше, поставщик данных не разделял названия маркеров на уникальные столбцы. Все столы сложены друг на друга. Что я хочу сделать, это преобразовать данные в это:

marker_name    group_no  group          1    2    3    4    5    6    a    b    c    d    e    f    g
marker1        GR-01-1   1              -    B    A    -    B
marker2        GR-01-1   1              -    A    B    -    -
marker3        GR-01-1   1              A    B    -    -    B
marker4        GR-01-1a  2              B    B    A    A
marker5        GR-01-1a  2              -    A    B    A
marker6        GR-01-1a  2              A    -    -    A
marker7        GR-01-1a  2              -    B    B    A
marker8        GR-01-2   3              B    A    -
marker9        GR-02-1   4              B    A    -    B    A    -
marker10       GR-02-1   4              A    A    B    B    B    A
marker11       GR-02-2   5                                                           B    A    B    -
marker12       GR-02-2   5                                                           B    B    -    B
marker13       GR-02-2   5                                                           A    B    -    -

Есть ли способ сделать это в R? A l oop возможно? Я начал с транспонирования в R, но это не сработало, и мне интересно, возможно, был способ прочитать данные с помощью group_no. Но не повезло. Я все еще новичок, я думаю. В одном наборе данных 917 таблиц. Я надеюсь, что мне не нужно присваивать каждый новый объект R один за другим, а затем rbind или cbind.

Answer 1

#Reading data into R
library(readr) 
df1 <- read_csv("C:/Users/userm/Desktop/df1.csv", 
                col_names = FALSE)

#Loading libraries:
library(plyr)
library(tidyr)

spl <- diff(c(which(df1$X1 == 'group_no'), nrow(df1))) #defining the split for each table

#Splitting to a list of dataframes, where each dataframe is one of the tables of interest:
dl2 <- split(df1, 
            c(rep(1, spl[1]),
              rep(2, spl[2]),
              rep(3, spl[3]),
              rep(4, spl[4]),
              rep(5, spl[5])))

#Assigning the first row as the dataframe header:
dl3 <- lapply(dl2, function(d){colnames(d) <- d[1,]; d <- d[-1,]})

#Removing columns with All NAs:
dl4 <- lapply(dl3, function(d){d <- d[,colSums(is.na(d))<nrow(d)]})

#Binding dataframes with different number of columns (plyr):
df5 <- rbind.fill(dl4)

#Converting from Wide to Long (tidyr):
df6 <- pivot_longer(df5, -c("group_no", "group", "variable"), 
                          names_to = "marker_name", values_to = "value")

#Convert from Long to Wide with a different arrangement (tidyr):
df7 <- pivot_wider(df6, names_from = "variable", values_from = "value")

#> # A tibble: 65 x 16
#>    group_no group marker_name a     b     c     `4`   `5`   g     `1`  
#>    <chr>    <chr> <chr>       <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#>  1 1        GR-0~ marker1     -     B     A     -     B     <NA>  <NA> 
#>  2 1        GR-0~ marker2     -     A     B     -     -     <NA>  <NA> 
#>  3 1        GR-0~ marker3     A     B     -     -     B     <NA>  <NA> 
#>  4 1        GR-0~ marker4     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#>  5 1        GR-0~ marker5     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#>  6 1        GR-0~ marker6     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#>  7 1        GR-0~ marker7     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#>  8 1        GR-0~ marker8     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#>  9 1        GR-0~ marker9     <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#> 10 1        GR-0~ marker10    <NA>  <NA>  <NA>  <NA>  <NA>  <NA>  <NA> 
#> # ... with 55 more rows, and 6 more variables: `2` <chr>, `3` <chr>,
#> #   `6` <chr>, d <chr>, e <chr>, f <chr>

Данные:

df1 <- structure(list(X1 = c("group_no", "1", "1", "1", "1", "1", "group_no", 
"2", "2", "2", "2", "group_no", "3", "3", "3", "group_no", "4", 
"4", "4", "4", "4", "4", "group_no", "5", "5", "5", "5"), X2 = c("group", 
"GR-01-1", "GR-01-1", "GR-01-1", "GR-01-1", "GR-01-1", "group", 
"GR-01-1a", "GR-01-1a", "GR-01-1a", "GR-01-1a", "group", "GR-01-2", 
"GR-01-2", "GR-01-2", "group", "GR-02-1", "GR-02-1", "GR-02-1", 
"GR-02-1", "GR-02-1", "GR-02-1", "group", "GR-02-2", "GR-02-2", 
"GR-02-2", "GR-02-2"), X3 = c("variable", "a", "b", "c", "4", 
"5", "variable", "1", "2", "3", "4", "variable", "1", "2", "3", 
"variable", "1", "2", "3", "4", "5", "6", "variable", "d", "e", 
"f", "g"), X4 = c("marker1", "-", "B", "A", "-", "B", "marker4", 
"B", "B", "A", "A", "marker8", "B", "A", "-", "marker9", "B", 
"A", "-", "B", "A", "-", "marker11", "B", "A", "B", "-"), X5 = c("marker2", 
"-", "A", "B", "-", "-", "marker5", "-", "A", "B", "A", NA, NA, 
NA, NA, "marker10", "A", "A", "B", "B", "B", "A", "marker12", 
"B", "B", "-", "B"), X6 = c("marker3", "A", "B", "-", "-", "B", 
"marker6", "A", "-", "-", "A", NA, NA, NA, NA, NA, NA, NA, NA, 
NA, NA, NA, "marker13", "A", "B", "-", "-"), X7 = c(NA, NA, NA, 
NA, NA, NA, "marker7", "-", "B", "B", "A", NA, NA, NA, NA, NA, 
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA)), class = c("spec_tbl_df", 
"tbl_df", "tbl", "data.frame"), row.names = c(NA, -27L), spec = structure(list(
    cols = list(X1 = structure(list(), class = c("collector_character", 
    "collector")), X2 = structure(list(), class = c("collector_character", 
    "collector")), X3 = structure(list(), class = c("collector_character", 
    "collector")), X4 = structure(list(), class = c("collector_character", 
    "collector")), X5 = structure(list(), class = c("collector_character", 
    "collector")), X6 = structure(list(), class = c("collector_character", 
    "collector")), X7 = structure(list(), class = c("collector_character", 
    "collector"))), default = structure(list(), class = c("collector_guess", 
    "collector")), skip = 0), class = "col_spec"))

   X1       X2       X3       X4      X5      X6      X7     
 1 group_no group    variable marker1 marker2 marker3 NA     
 2 1        GR-01-1  a        -       -       A       NA     
 3 1        GR-01-1  b        B       A       B       NA     
 4 1        GR-01-1  c        A       B       -       NA     
 5 1        GR-01-1  4        -       -       -       NA     
 6 1        GR-01-1  5        B       -       B       NA     
 7 group_no group    variable marker4 marker5 marker6 marker7
 8 2        GR-01-1a 1        B       -       A       -      
 9 2        GR-01-1a 2        B       A       -       B      
10 2        GR-01-1a 3        A       B       -       B    
# ... with 17 more rows