annotation class and methods

annotation objects are used to describe dna_seg objects. It consists of labels that are attached to a single position or a range.

Usage

annotation(x1, x2 = NA, text, rot = 0, col = "black")

as.annotation(df, x2 = NA, rot = 0, col = "black")

is.annotation(annotation)

Arguments

x1: A numeric vector giving the first or only position of the label.
x2: A numeric vector of the same length as x1 or NA, providing an optional secondary position for the label.
text: A character vector of the same length as x1, providing the text of the labels.
rot: A numeric vector of the same length as x1, providing the rotation of the labels in degrees.
col: A character vector of the same length as x1, providing the color of the labels.
df: A data.frame to convert to an annotation object. Must have at least the columns x1 and text.
annotation: An object to test.

Value

as.annotation and annotation both return an annotation object.

is.annotation returns a logical.

Details

An annotation object is a data.table with the columns x1, x2, text, col, and rot. These provide the first (or only) position, an optional second position, the text, the color, and the rotation of the annotation, respectively.

When plotted using plot_gene_map, it will add an annotation row on top of the corresponding DNA segment. For any given row of an annotation object, if x2 is NA, the label will be attached to the position given by x1. If x2 is a number instead, a range will be plotted between these two values and the label itself will be attached in the middle of this range.

is.annotation returns TRUE if the object tested is an annotation object.

Author

Lionel Guy

Examples

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

## Calculating middle positions
mid_pos <- middle(dna_segs[[1]])

## Create first annotation
annot1 <- annotation(x1 = mid_pos, text = dna_segs[[1]]$name)
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons,
              annotations = annot1)


## Exploring options
annot2 <- annotation(x1 = c(mid_pos[1], dna_segs[[1]]$end[2]),
                     x2 = c(NA, dna_segs[[1]]$end[3]),
                     text = c(dna_segs[[1]]$name[1], "region1"),
                     rot = c(30, 0),
                     col = c("grey", "black"))
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons,
              annotations = annot2, annotation_height = 1.3)

              
## Using a bigger dataset from a 4-genome comparison
data(barto)

## Showing several subsegments
xlims2 <- list(c(1445000, 1415000, 1380000, 1412000),
               c(  10000,   45000,   50000,   83000, 90000, 120000),
               c(  15000,   36000,   90000,  120000, 74000,  98000),
               c(   5000,    82000))
## Adding annotations for all genomes, allow segments to be placed out
## of the longest segment
annots <- lapply(barto$dna_segs, function(x) {
  mid <- middle(x)
  annot <- annotation(x1 = mid, text = x$name, rot = 30)
  # removing gene names starting with "B" and keeping 1 in 4
  idx <- grep("^[^B]", annot$text, perl = TRUE)
  annot[idx[idx %% 4 == 0], ]
})
plot_gene_map(dna_segs = barto$dna_segs,
              comparisons = barto$comparisons,
              annotations = annots,
              xlims = xlims2,
              limit_to_longest_dna_seg = FALSE,
              dna_seg_scale = TRUE)


## Annotations on all the segments
annots <- lapply(dna_segs, function(x) {
  mid <- middle(x)
  annot <- annotation(x1 = mid, text = x$name, rot = 30)
})
plot_gene_map(dna_segs = dna_segs,
              comparisons = comparisons,
              annotations = annots,
              annotation_height = 1.8,
              annotation_cex = 1)