Auto-annotate dna_segs

Annotate dna_segs in a smart way. This is especially designed for dna_segs read from GenBank or EMBL files, but can be used for other purposes as well. With the default arguments, it produces annotation objects based on the gene attribute of dna_segs.

Usage

auto_annotate(
  dna_seg_input,
  names = "gene",
  basic_mode = FALSE,
  locus_tag_pattern = NULL,
  keep_genes_only = TRUE,
  dna_seg = NULL,
  ...
)

Arguments

dna_seg_input: Either a single dna_seg or a list of dna_seg objects.
names: A character string with the name of a dna_seg attribute, to base the annotations on. If dna_seg_input is a single dna_seg, it can also be a character vector with as many elements as there are rows in that dna_seg.
basic_mode: Logical. If TRUE, annotate the dna_seg_input using the names argument, ignoring all other arguments and never generating spanning annotations.
locus_tag_pattern: A character string giving a pattern, used to simplify names. To turn this off, use locus_tag_pattern = "". See details.
keep_genes_only: Logical. If TRUE, then for any row where names is "-", "NA", or empty (""), no annotations will be made. See details.
dna_seg: Deprecated, included for backwards compatibility. When provided, replaces dna_seg_input. it.
...: Further arguments to be passed to the annotation function, like rot or col.

Value

If dna_seg_input is a single dna_seg, then a single annotation object will be returned.

If dna_seg_input is a list of dna_seg objects, a list of annotation objects will be returned of equal length.

Details

keep_genes_only is intended to be used with the gene column. When TRUE, it will only make annotations for names that are not 'empty' ("-", "NA", or ""). When it is FALSE however, locus_tag_pattern becomes relevant. For any element of names that is 'empty', it will take the name attribute of the dna_seg and remove the locus_tag_pattern from it (e.g. Eco003456 becomes 003456, with Eco as the locus_tag_pattern). If locus_tag_pattern is left as NULL it will attempt to determine a common prefix automatically. To turn this behavior off, use locus_tag_pattern = "".

If names refers to gene names, it will create spanning annotations for operons or sequences of genes. For this to work, gene names have to be consecutive and end with a number or capital letter.

Author

Lionel Guy, Mike Puijk

Examples

## Prepare dna_seg
names <- paste("Eco", sprintf("%04d", 1:20), sep = "")
gene <- c("-", "atpC", "atpB", "atpA", "atp2", 
          "-", "-", "cda1", "cda2", "cda3",
          "vcx23", "vcx22", "vcx21", "cde20",
          "-", "gfrU", "gfrT", "gfrY", "gfrX", "gfrW")
ds <- dna_seg(data.frame(name = names,
                         start = (1:20) * 3,
                         end = (1:20) * 3 + 2,
                         strand = rep(1, 20),
                         gene = gene,
                         stringsAsFactors = FALSE))

## Original annotation
annot1 <- annotation(x1 = middle(ds), text = ds$gene, rot = 45)

## auto_annotate with various options
annot2 <- auto_annotate(ds)
annot3 <- auto_annotate(ds, keep_genes_only = FALSE,
                        locus_tag_pattern = "", rot = 75)
annot4 <- auto_annotate(ds, keep_genes_only = FALSE, col = "red")

## Plot
plot_gene_map(dna_segs = list(ds, ds, ds, ds),
              annotations = list(annot1, annot2, annot3, annot4))