# Apply a color scheme Apply a color scheme to a numeric vector, eventually taking the direction into account. ```r apply_color_scheme(x, direction = NULL, color_scheme = "grey", decreasing = FALSE, rng = NULL, transparency = 0.5) ``` ## Arguments - `x`: A numeric, that will be used to apply a gradient of colors to a comparison. - `direction`: If a red-blue scheme is choosen, the vector (composed of -1 and 1 values and of same length as `x`) giving the direction of the comparison. - `color_scheme`: Character. One of `red_blue`, `blue_red`, `grey`, `gray`. - `decreasing`: Logical. Are the values of the comparisons oriented such as the lower the value, the closer the relationship (e.g. e-values, gaps, mismatches, etc)? `FALSE` by default. - `rng`: Numeric of length 2. Gives the higher and lower limit to apply a color scheme. - `transparency`: Numeric of length 1, between 0 and 1, or FALSE. Should the color scheme use transparency, and if yes how much (ratio). 0.5 by default. Not supported on all devices. ## Details A color scale is calculated, with the darker color corresponding to the highest values of `x`, or the contrary is `decreasing` is `TRUE`. For the moment, two schemes (red-blue and grey scale) are used. For the red-blue scale (as in ACT), the direct comparisons are colored in red hues, and the reversed ones in blue hues. This is especially useful to replace comparison values (such as BLAST percent identity values) by color hues. ## Returns A character vector of same length as `x`, representing colors. ## References Artemis Comparison Tool, [https://www.sanger.ac.uk/tool/artemis-comparison-tool-act/](https://www.sanger.ac.uk/tool/artemis-comparison-tool-act/) ## Author(s) Lionel Guy ## See Also `comparison` ## Examples ```r ## Load data data(three_genes) ## Color schemes ## Greys comparisons[[1]]$values <- c(70, 80, 90) comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, color_scheme="grey") plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) ## Red-blue comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, direction=comparisons[[1]]$direction, color_scheme="red_blue") plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) ## Decreasing comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, direction=comparisons[[1]]$direction, color_scheme="red_blue", decreasing=TRUE) plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) ## Range comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, direction=comparisons[[1]]$direction, color_scheme="red_blue", rng=c(30,100)) plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) ## Transparency x1 <- seq(100, 600, by=50) x2 <- seq(1100, 700, by=-50) comparisons[[2]] <- as.comparison(data.frame(start1=c(x1, x2), end1=c(x1+250, x2+300), start2=c(x1+150, x2-300)+2000, end2=c(x1+250, x2-500)+2000 )) comparisons[[2]]$col <- apply_color_scheme(1:nrow(comparisons[[2]]), comparisons[[2]]$direction, color_scheme="blue_red") comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, color_scheme="grey", transparency=0.8) plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) comparisons[[1]]$col <- apply_color_scheme(comparisons[[1]]$values, color_scheme="grey", transparency=1) comparisons[[2]]$col <- apply_color_scheme(1:nrow(comparisons[[2]]), comparisons[[2]]$direction, color_scheme="blue_red", transparency=0.2) plot_gene_map(dna_segs=dna_segs, comparisons=comparisons) ```

apply_color_scheme function