Reverse objects

Reverses objects, mainly meant for dna_seg and comparison objects.

Usage

reverse(x, ...)

# Default S3 method
reverse(x, ...)

# S3 method for class 'dna_seg'
reverse(x, ...)

# S3 method for class 'comparison'
reverse(x, side = 0, ...)

Arguments

x

An object to reverse.

...

Unused.

side

Used only when x is a comparison object, the side that should be reversed. If side = 1, the first side will be reversed. If side = 2, the second side will be reversed. If side < 1, no side is reversed. If side > 2, both sides are reversed.

Value

An object with the same type as x.

See also

dna_seg, comparison

Author

Lionel Guy

Examples

## load data
data(three_genes)
dna_segs <- three_genes$dna_segs
comparisons <- three_genes$comparisons

## on dna_seg
dna_segs[[1]]
#>      name start   end strand   fill gene_type region_plot    col   lty   lwd
#>    <char> <num> <num>  <num> <char>    <char>      <char> <char> <num> <num>
#> 1:  feat1     2   600     -1   blue    arrows          NA gray20     1     1
#> 2:  feat2  1000   800     -1   grey    arrows          NA gray20     1     1
#> 3:  feat3  1050  1345      1    red    arrows          NA gray20     1     1
#>      pch   cex
#>    <num> <num>
#> 1:     8     1
#> 2:     8     1
#> 3:     8     1
reverse(dna_segs[[1]])
#>      name start   end strand   fill gene_type region_plot    col   lty   lwd
#>    <char> <num> <num>  <num> <char>    <char>      <char> <char> <num> <num>
#> 1:  feat1  -600    -2      1   blue    arrows          NA gray20     1     1
#> 2:  feat2  -800 -1000      1   grey    arrows          NA gray20     1     1
#> 3:  feat3 -1345 -1050     -1    red    arrows          NA gray20     1     1
#>      pch   cex
#>    <num> <num>
#> 1:     8     1
#> 2:     8     1
#> 3:     8     1
## on comparison
reverse(comparisons[[2]], side = 1)
#>    start1  end1 start2  end2     col direction
#>     <num> <num>  <num> <num>  <char>     <num>
#> 1:    -50  -500   1899  2034 #67000D        -1
#> 2:   -800 -1100   2732  2508 #08306B         1
reverse(comparisons[[2]], side = 3)
#>    start1  end1 start2  end2     col direction
#>     <num> <num>  <num> <num>  <char>     <num>
#> 1:    -50  -500  -1899 -2034 #67000D         1
#> 2:   -800 -1100  -2732 -2508 #08306B        -1

## With mauve backbone
data(mauve_bbone)
## Plot
plot_gene_map(dna_segs = mauve_bbone$dna_segs,
              comparisons = mauve_bbone$comparisons,
              alpha_comparisons = 0.4)


## Reverse B_bacilliformis, and the corresponding comparison (first "side")
mauve_bbone$dna_segs[[1]] <- reverse(mauve_bbone$dna_segs[[1]])
mauve_bbone$comparisons[[1]] <- reverse(mauve_bbone$comparisons[[1]], 1)
plot_gene_map(dna_segs = mauve_bbone$dna_segs,
              comparisons = mauve_bbone$comparisons,
              alpha_comparisons = 0.4)