Menu
Given a data frame dna
> dna
chrom start
chr2 39482
chr1 203918
chr1 198282
chrX 7839028
chr17 3874
The following code reorders dna by $chrom in alphabetical ascending order and by $start in numerical ascending order:
> dna <- dna[with(dna, order(chrom, start)), ]
> dna
chrom start
chr1 198282
chr1 203918
chr17 3874
chr2 39482
chrX 7839028
However, I would like to be able to have $chrom ordered as follows (simplified for the sake of my example here):
chrom_order <- c("chr1","chr2", "chr17", "chrX")
I am not allowed to rename stuff, for example chr1 to chr01.
874
To sort a data frame in R, use the order( ) function. By default, sorting is ASCENDING.
The arrange() function lets you reorder the rows of a tibble. It takes a tibble, followed by the unquoted names of columns. For example, to sort in ascending order of the values of column x , then (where there is a tie in x ) by descending order of values of y , you would write the following.
To sort the DataFrame based on the values in a single column, you'll use . sort_values() . By default, this will return a new DataFrame sorted in ascending order. It does not modify the original DataFrame.
You need to specify the levels in factor and then use order with indexing:
zz <- "chrom start
chr2 39482
chr1 203918
chr1 198282
chrX 7839028
chr17 3874"
Data <- read.table(text=zz, header = TRUE)
library(Hmisc)
library(gdata)
Data$chrom <- reorder.factor(Data$chrom , levels = c("chr1","chr2", "chr17", "chrX"))
Data[order(Data$chrom), ]
chrom start
2 chr1 203918
3 chr1 198282
1 chr2 39482
5 chr17 3874
4 chrX 7839028
or you can use this:
> Data$chrom <- factor(chrom , levels = c("chr1","chr2", "chr17", "chrX"))
> Data[order(Data$chrom), ]
chrom start
2 chr1 203918
3 chr1 198282
1 chr2 39482
5 chr17 3874
4 chrX 7839028
or use this:
> Data$chrom <- reorder(Data$chrom, new.order=c("chr1","chr2", "chr17", "chrX"))
> Data[order(Data$chrom), ]
Try this:
dna <- structure(list(chrom = structure(c(2L, 1L, 1L, 4L, 3L), .Label = c("chr1",
"chr2", "chr17", "chrX"), class = c("ordered", "factor")), start = c(39482L,
203918L, 198282L, 7839028L, 3874L)), .Names = c("chrom", "start"
), row.names = c(NA, -5L), class = "data.frame")
chrom_order <- c("chr1","chr2", "chr17", "chrX")
# Make chrom column ordered. Second term defines the order
dna$chrom <- ordered(dna$chrom, chrom_order)
dna[with(dna, order(chrom, start)),]
chrom start
3 chr1 198282
2 chr1 203918
1 chr2 39482
5 chr17 3874
4 chrX 7839028
If you love us? You can donate to us via Paypal or buy me a coffee so we can maintain and grow! Thank you!
Donate Us With
