# Gene types Returns a vector containing the available gene types. In addition to these gene types, the user can provide graphical functions that return a list or a single `grob` object. ```r gene_types(auto = TRUE) ``` ## Arguments - `auto`: Logical. Should type "auto" be added? ## Returns A character vector. ## Details `dna_seg`s may contain one character column `gene_type`. Elements in this column should either be one of the predefined gene types, or refer to a graphical function that has exactly the same name and that returns a `grob` or a `gList` object. A gene object (i.e. a single row of a `dna_seg`) is passed to the graphical function, as well as the contents of the `...`. The start and line width of an element can thus be accessed via `gene$start` and `gene$lwd`. Extra columns that would be added in the `dna_seg` can be used similarly. Extra arguments can also be globally passed via `...` when calling `plot_gene_map`. ## Author(s) Lionel Guy ## See Also `plot_gene_map`, `dna_seg` ## Examples ```r ## To view pre-coded gene types: gene_types() ## Load data data(barto) n <- length(gene_types(auto=FALSE)) ## Get a small subset from the barto dataset dna_seg <- barto$dna_segs[[3]][1:n,] plot_gene_map(list(dna_seg)) ## Change gene_types and plot again dna_seg$gene_type <- gene_types(auto=FALSE) dna_seg$fill <- rainbow(n) dna_seg_r <- dna_seg dna_seg_r$strand <- -dna_seg$strand ## Add an annotation annot <- annotation(middle(dna_seg), text=dna_seg$gene_type, rot=45, col=dna_seg$col) ## Plot plot_gene_map(list(dna_seg, dna_seg_r), annotations=list(annot, annot), annotation_height=5, dna_seg_line=grey(0.7)) ## Using home-made graphical functions ## Data data(three_genes) ## Functions returning grobs. ## Creates a triangle triangleGrob <- function(gene, ...) { x <- c(gene$start, (gene$start+gene$end)/2, gene$end) y1 <- 0.5 + 0.4*gene$strand y <- c(y1, 0.5, y1) polygonGrob(x, y, gp=gpar(fill=gene$fill, col=gene$col, lty=gene$lty, lwd=gene$lwd), default.units="native") } ## Draws a star. Note that the limits of the dna_seg region are ## voluntarily not respected starGrob <- function(gene, ...){ ## Coordinates for the star x <- sin(((0:5)/2.5)*pi)*(gene$end-gene$start)/2 + (gene$end+gene$start)/2 y <- cos(((0:5)/2.5)*pi)*gene$strand*2 + 0.5 idx <- c(1, 3, 5, 2, 4, 1) ## Attribute line_col only if present in the gene line_col <- if (!is.null(gene$line_col)) gene$line_col else gene$col ## Having a conditional transparency, depending on a length cut-off ## passed via dots length_cutoff <- list(...)$length_cutoff if (!is.null(length_cutoff)){ alpha <- if ((gene$end-gene$start) < length_cutoff) 0.3 else 0.8 } else alpha <- 1 ## Grobs g <- polygonGrob(x[idx], y[idx], gp=gpar(fill=gene$col, col=line_col, lty=gene$lty, lwd=gene$lwd, alpha=alpha), default.units="native") t <- textGrob(label="***", x=(gene$end+gene$start)/2, y=0.5, default.units="native") gList(g, t) } ## Replacing the standard types dna_segs[[1]]$gene_type <- "triangleGrob" dna_segs[[2]]$gene_type <- "starGrob" ## Adding more variables dna_segs[[2]]$line_col <- c("black", grey(0.3), "blue") ## Mix of several types on the same line dna_segs[[3]]$gene_type <- c("starGrob", "triangleGrob", "arrows") ## Plot plot_gene_map(dna_segs, comparisons, length_cutoff=600) ```

gene_types function