通过按字母顺序仅对行中的一些字段进行排序来重塑R中的数据帧 [英] Reshaping a dataframe in R by sorting just some fields in a row alphabetically

问题描述

我在RStudio中有几个大型数据帧，它们的结构如下：

Original data structure

structure(list(CHROM = c("scaffold1000|size223437", "scaffold1000|size223437", 
"scaffold1000|size223437", "scaffold1000|size223437"), POS = c(666, 
1332, 3445, 4336), REF = c("A", "TA", "CTTGA", "GCTA"), RO = c(20, 
14, 9, 25), ALT_1 = c("GAT", "TGC", "AGC", "T"), ALT_2 = c("CAG", 
"TGA", "CGC", NA), ALT_3 = c("G", NA, "TGA", NA), ALT_4 = c("AGT", 
NA, NA, NA), AO_1 = c(13, 4, 67, 120), AO_2 = c(12, 5, 34, NA
), AO_3 = c(6, NA, 18, NA), AO_4 = c(101, NA, NA, NA), AOF_1 = c(8.55263157894737, 
17.3913043478261, 52.34375, 82.7586206896552), AOF_2 = c(7.89473684210526, 
21.7391304347826, 26.5625, NA), AOF_3 = c(3.94736842105263, NA, 
14.0625, NA), AOF_4 = c(66.4473684210526, NA, NA, NA)), class = "data.frame", row.names = c(NA, 
-4L))

但对于分析，我需要它看起来像这样：

Desired output

 structure(list(CHROM = c("scaffold1000|size223437", "scaffold1000|size223437", 
    "scaffold1000|size223437", "scaffold1000|size223437"), POS = c(666, 
    1332, 3445, 4336), REF = c("A", "TA", "CTTGA", "GCTA"), RO = c(20, 
    14, 9, 25), ALT_1 = c("AGT", "TGA", "AGC", "T"), ALT_2 = c("CAG", 
    "TGC", "CGC", NA), ALT_3 = c("G", NA, "TGA", NA), ALT_4 = c("GAT", 
    NA, NA, NA), AO_1 = c(101, 5, 67, 120), AO_2 = c(12, 4, 34, NA
    ), AO_3 = c(6, NA, 18, NA), AO_4 = c(13, NA, NA, NA), AOF_1 = c(66.4473684210526, 
    21.7391304347826, 52.34375, 82.7586206896552), AOF_2 = c(7.89473684210526, 
    17.3913043478261, 26.5625, NA), AOF_3 = c(3.94736842105263, NA, 
    14.0625, NA), AOF_4 = c(8.55263157894737, NA, NA, NA)), class = "data.frame", row.names = c(NA, 
    -4L))

因此，我想要做的是以某种方式重新排列行的内容，即按字母顺序对列ALT_1、ALT_2、ALT_3、ALT_4进行排序，但同时我还需要重新排列对应的AO和AOF列，以便值仍然匹配。 (AO_1的值仍应与ALT_1中的序列匹配。 因此，如果在排序的数据帧中ALT_1变为ALT_2，则AO_1也应变为AO_2)

我到目前为止所做的尝试，但不起作用：

将ALT_1、AO_1、AOF_1的值都粘贴到一个字段中，因此我将它们与

  if (is.na(X[i,6]) == FALSE) {
    X[i,6] <- paste(X[i,6],X[i,10],X[i,14],sep=" ")
  }
}

然后我想提取每一行作为向量来对值进行排序并将其放回数据帧中，但我没能做到这一点。

因此，问题将是如何对数据帧进行排序以获得所需的输出？ (我需要将此应用于32个数据帧，每个数据帧具有>；100.000个值)

推荐答案

以下是dplyr解决方案。花了我一些时间，我需要一些帮助pivot_wider dissolves arrange：

library(dplyr)
library(tidyr)

df1 %>% 
  mutate(id = row_number()) %>% 
  unite("conc1", c(ALT_1, AO_1, AOF_1), sep = "_") %>% 
  unite("conc2", c(ALT_2, AO_2, AOF_2), sep = "_") %>% 
  unite("conc3", c(ALT_3, AO_3, AOF_3), sep = "_") %>% 
  unite("conc4", c(ALT_4, AO_4, AOF_4), sep = "_") %>% 
  pivot_longer(
    starts_with("conc")
  ) %>% 
  mutate(value = ifelse(value=="NA_NA_NA", NA_character_, value)) %>% 
  group_by(id) %>% 
  mutate(value = sort(value, na.last = TRUE)) %>% 
  ungroup() %>% 
  pivot_wider(
    names_from = name,
    values_from = value,
    values_fill = "0"
  ) %>% 
  separate(conc1, c("ALT_1", "AO_1", "AOF_1"), sep = "_") %>% 
  separate(conc2, c("ALT_2", "AO_2", "AOF_2"), sep = "_") %>% 
  separate(conc3, c("ALT_3", "AO_3", "AOF_3"), sep = "_") %>% 
  separate(conc4, c("ALT_4", "AO_4", "AOF_4"), sep = "_") %>% 
  select(CHROM, POS, REF, RO, starts_with("ALT"), starts_with("AO_"), starts_with("AOF_")) %>% 
  type.convert(as.is=TRUE)

  CHROM                     POS REF      RO ALT_1 ALT_2 ALT_3 ALT_4  AO_1  AO_2  AO_3  AO_4 AOF_1 AOF_2 AOF_3 AOF_4
  <chr>                   <int> <chr> <int> <chr> <chr> <chr> <chr> <int> <int> <int> <int> <dbl> <dbl> <dbl> <dbl>
1 scaffold1000|size223437   666 A        20 AGT   CAG   G     GAT     101    12     6    13  66.4  7.89  3.95  8.55
2 scaffold1000|size223437  1332 TA       14 TGA   TGC   NA    NA        5     4    NA    NA  21.7 17.4  NA    NA   
3 scaffold1000|size223437  3445 CTTGA     9 AGC   CGC   TGA   NA       67    34    18    NA  52.3 26.6  14.1  NA   
4 scaffold1000|size223437  4336 GCTA     25 T     NA    NA    NA      120    NA    NA    NA  82.8 NA    NA    NA   

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