Two methods of chromosome coordinate sequencing

This problem is often encountered when drawing , There are some NGS Software will also encounter . Use the following code to simulate the data

pos_df=do.call(rbind,lapply(1:10, function(i){
  data.frame(gene=paste0('gene',i,LETTERS),
             chr=sample(paste0('chr',1:22),26,replace = T),
             start= sample(1:1000,26))
}))
pos_df=pos_df[with(pos_df,order(chr,start)),]
pos_df$chr=as.factor(pos_df$chr)
plot(pos_df$chr,pos_df$start,las=2)

First of all, our sequencing is not in chromosome order , It is

> levels((pos_df$chr))
 [1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16"
 [9] "chr17" "chr18" "chr19" "chr2"  "chr20" "chr21" "chr22" "chr3" 
[17] "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9" 
> 

In this case sort This vector is actually meaningless , There are two solutions to it ！

The first is to set the level of the factor