I have a few large dataframes in RStudio, that have this 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))
But for an analysis I need it to look like this:
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))
So what I would like to do is to rearrange the content of a row in a way, that the columns ALT_1, ALT_2, ALT_3, ALT_4 are alphabetically sorted, but at the same time I also need to rearrange the corresponding columns of AO and AOF, so that the values still match. (The value of AO_1 should still match with the sequence that was in ALT_1. So if ALT_1 becomes ALT_2 in the sorted dataframe, AO_1 should also become AO_2)
What I tried so far, but didn't work:
Pasting the values of ALT_1, AO_1, AOF_1 all in one field, so I have them together with
if (is.na(X[i,6]) == FALSE) {
X[i,6] <- paste(X[i,6],X[i,10],X[i,14],sep=" ")
}
}
And then I wanted to extract every row as a vector to sort the values and put it back in the dataframe, but I didn't manage to do this.
So the question would be how I can order the dataframe to get the desired output? (I need to apply this to 32 dataframes with each having >100.000 values)
Here is dplyr solution. Took me some time and I needed some help 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