dna_seg class and methods

dna_seg objects are collections of genes or other elements along a genome, to be represented on a map. These functions are class functions to create, convert, and test dna_seg objects.

Usage

dna_seg(x, ...)

as.dna_seg(
  df,
  col = "grey20",
  fill = "grey80",
  lty = 1,
  lwd = 1,
  pch = 8,
  cex = 1,
  gene_type = "arrows",
  region_plot = "NA",
  ordered = TRUE
)

is.dna_seg(dna_seg)

Arguments

x: An object to be coerced. Can be a data.frame, data.table, or list object. See details for necessary columns.
...: Arguments to pass to dna_seg, see arguments below.
df: Same as x.
col: A character vector of colors, of either length one or the same length as x. Determines the outline of features, or their overall color for shapes (see gene_types) that have no fill color (e.g. text, points).
fill: Same as col, but determines the fill color of features.
lty: A vector of either length 1 or the same length as x. Determines the line type (see par) of the features.
lwd: A numeric vector of either length 1 or the same length as x. Determines the line width (see par) of the features.
pch: A vector of either length 1 or the same length as x. Determines the shape (see points) of the features when they are represented by points.
cex: A numeric vector of either length 1 or same the length as x. Determines the size multiplier of features when they are represented by text or points.
gene_type: A character vector of either length 1 or same the length as x. Determines the gene type (i.e. shape) of the features. See gene_types.
region_plot: A character vector of either length 1 or the same length as x. Determines if features are going to be plotted when going for regional plotting. See plot_gene_map for more details.
ordered: Logical. If TRUE, orders the dna_seg on the start and end columns.
dna_seg: An object to test.

Value

as.dna_seg and dna_seg both return a dna_seg object.

is.dna_seg returns a logical.

Details

A dna_seg object is a data.table that must start with the columns name, start, end, and strand. The arguments listed above add more columns, but only if those were not already present in the data provided by x. Any number of additional columns can be added to dna_seg objects, to act as metadata or as ways to group or identify features.

dna_seg and as.dna_seg can both be used to create dna_seg objects from list, data.frame, or data.table objects. Alternatively, read_dna_seg_from_file can be used to create them from a file.

These objects inherit from data.table, and can therefore be manipulated using data.table syntax.

is.dna_seg returns TRUE if the object tested is a dna_seg object.

Author

Lionel Guy, Mike Puijk

Examples

## Generate data
names1 <- c("feat1", "feat2", "feat3")
starts1 <- c(2, 1000, 1050)
ends1 <- c(600, 800, 1345)
strands1 <- c("-", -1, 1)
cols1 <- c("blue", "grey", "red")

## Create data.frame
df1 <- data.frame(name = names1, start = starts1, end = ends1,
                  strand = strands1, col = cols1)

## Create dna_seg
dna_seg1 <- dna_seg(df1)
dna_seg1
#>      name start   end strand    col gene_type region_plot   fill   lty   lwd
#>    <char> <num> <num>  <num> <char>    <char>      <char> <char> <num> <num>
#> 1:  feat1     2   600     -1   blue    arrows          NA grey80     1     1
#> 2:  feat2  1000   800     -1   grey    arrows          NA grey80     1     1
#> 3:  feat3  1050  1345      1    red    arrows          NA grey80     1     1
#>      pch   cex
#>    <num> <num>
#> 1:     8     1
#> 2:     8     1
#> 3:     8     1
as.dna_seg(df1)
#>      name start   end strand    col gene_type region_plot   fill   lty   lwd
#>    <char> <num> <num>  <num> <char>    <char>      <char> <char> <num> <num>
#> 1:  feat1     2   600     -1   blue    arrows          NA grey80     1     1
#> 2:  feat2  1000   800     -1   grey    arrows          NA grey80     1     1
#> 3:  feat3  1050  1345      1    red    arrows          NA grey80     1     1
#>      pch   cex
#>    <num> <num>
#> 1:     8     1
#> 2:     8     1
#> 3:     8     1

## Test dna_seg
is.dna_seg(dna_seg1)
#> [1] TRUE