I should start by saying I have solved this problem, but I feel like my code is ugly and overkill.
I am trying to sort a dataframe on a column containing human chromosomes:
chr1,chr2...chrY, chrX.
the problem is:
chr1, is followed by chr10.
What tricks do you use to deal with this problem IN the [R] environment?
the mixedsort is pretty good, but it will think ChrM comes before ChrX, then ChrY
if you have your own arbitrary order you should just use factors
> df<-data.frame("chr"=c("chr1","chrM","chr10","chr2","chrX","chr2"),"val"=c(1,2,3,4,5,6))
> df
chr val
1 chr1 1
2 chrM 2
3 chr10 3
4 chr2 4
5 chrX 5
6 chr2 6
> chrOrder<-c(paste("chr",1:22,sep=""),"chrX","chrY","chrM")
> df$chr<-factor(df$chr, levels=chrOrder)
> df$chr
[1] chr1 chrM chr10 chr2 chrX chr2
Levels: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM
> df[order(df$chr),]
chr val
1 chr1 1
4 chr2 4
6 chr2 6
3 chr10 3
5 chrX 5
2 chrM 2
Hi Zev,
what you are looking for is: mixedsort {gtools}
Order or Sort strings with embedded numbers so that the numbers are in the correct order
package 'gtools' was built under R version 2.13.2
n<- c('chr1','chr21','chr13','chr4','chr10')
> n
[1] "chr1" "chr21" "chr13" "chr4" "chr10"
> mixedsort(n)
[1] "chr1" "chr4" "chr10" "chr13" "chr21"
I hope this helps.
You could substitute chr1 for chr01 (ie, zero-one), globally, but in that column.
