Lists gene_types for dna_seg objects

Returns a character vector containing the available gene types when plotting dna_seg features.

Usage

gene_types(auto = TRUE)

Arguments

auto: Logical. If TRUE, includes the "auto" gene type in the output, which has plot_gene_map determine what gene type to use automatically.

Value

A character vector.

Details

dna_segs may contain the gene_type column, which determines the shape of dna_seg features when they are plotted using plot_gene_map. Elements in this column should either be one of the predefined gene types returned by this function, or they must refer to a graphical function with exactly the same name that returns a grob or a gList object.

Author

Lionel Guy

Examples

## To view pre-coded gene types:
gene_types()
#>  [1] "auto"            "arrows"          "headless_arrows" "blocks"         
#>  [5] "bars"            "points"          "text"            "lines"          
#>  [9] "side_blocks"     "side_bars"       "side_points"     "side_text"      
#> [13] "side_lines"      "introns"         "exons"           "side_exons"     
#> [17] "boundaries"     

## 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))