# Annotation class and class functions An annotation describes a DNA segment. It has labels attached to positions. Each label can be attached to a single position or to a range. ```r annotation(x1, x2 = NA, text, rot = 0, col = "black") as.annotation(df, x2 = NA, rot = 0, col = "black") is.annotation(annotation) ``` ## Arguments - `x1`: Numeric. A vector giving the first or only position of the label. Mandatory. - `x2`: Numeric. A vector of the same length as `x1`. If a row (or the whole column is `NA`, then the annotation(s) will be attached to `x0`. Else, the annotation will be attached to the range between both positions. `NA` by default. - `text`: Character of the same length as `x0`. Gives the text of the labels. Mandatory. - `rot`: Numeric of the same length as `x0`. Gives the rotation, in degrees, of the labels. 0 by default. - `col`: Vector of the same length as `x0`. The color of the labels. `black` by default. - `df`: A data frame to convert to an annotation object. Should have at least columns `x1` and `text`. - `annotation`: An object to test. ## Details An `annotation` object is a data frame with columns `x0`, `x1`, `text`, `col` and `rot`. They give, respectively, the first (or only) position, eventually the second position, the text, the color and the rotation of the annotation. When plotted with `plot_gene_map`, it will add an annotation row on top of the first `dna_seg`. Labels for which only one position is given will be centered on that position. Labels for which two positions are given are linked by an horizontal square bracket and the label is plotted in the middle of the positions. ## Returns `annotation` and `as.annotation` return an annotation object. `is.annotation` returns a logical. ## Author(s) Lionel Guy ## See Also `plot_gene_map`, `middle`. ## Examples ```r ## loading data data(three_genes) ## 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) ## Annotations on all the segments annots <- lapply(dna_segs, function(x){ mid <- middle(x) annot <- annotation(x1=mid, text=x$name, rot=30) }) plot_gene_map(dna_segs=dna_segs, comparisons=comparisons, annotations=annots, annotation_height=1.8, annotation_cex=1) ## ## Using a bigger dataset from a 4-genome comparison ## data(barto) ## Adding a tree tree <- newick2phylog("(BB:2.5,(BG:1.8,(BH:1,BQ:0.8):1.9):3);") ## Showing several subsegments xlims2 <- list(c(1445000, 1415000, 1380000, 1412000), c( 10000, 45000, 50000, 83000, 90000, 120000), c( 15000, 36000, 90000, 120000, 74000, 98000), c( 5000, 82000)) ## Adding annotations for all genomes, allow segments to be placed out ## of the longest segment annots <- lapply(barto$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(barto$dna_segs, barto$comparisons, tree=tree, annotations=annots, xlims=xlims2, limit_to_longest_dna_seg=FALSE, dna_seg_scale=TRUE) ```

annotation function