Generate a gradient color scheme

A color scale is generated based on a numeric vector, with the darker colors corresponding to the higher values, or the lower values if decreasing = TRUE.

Usage

gradient_color_scheme(
  x,
  direction = NULL,
  color_scheme = "grey",
  decreasing = FALSE,
  rng = NULL,
  alpha = 0.5,
  transparency
)

apply_color_scheme(
  x,
  direction = NULL,
  color_scheme = "grey",
  decreasing = FALSE,
  rng = NULL,
  alpha = 0.5,
  transparency
)

Arguments

x: A numeric vector to generate colors for.
direction: A numeric vector composed of -1 and 1 values, denoting the direction of the comparison. Ignored unless the color scheme is a red-blue color scheme.
color_scheme: A character string, one of: "red_blue", "blue_red", "gray", or "grey".
decreasing: Logical. Are the values of x representing a relationship that gets stronger as the number goes down (e.g. e-values, gaps, mismatches)?
rng: Numeric of length 2. Gives the lower and upper limits to apply the gradient to.
alpha: A single numeric value between 0 and 1, or FALSE. Determines the transparency applied to the color scheme, 0 being fully transparent, and 1 being fully opaque.
transparency: Deprecated, included for backwards compatibility. When provided, replaces alpha.

Value

A character vector of colors, with the same length as x.

Details

apply_color_scheme is synonymous with gradient_color_scheme, and is included for backwards compatibility.

Made for use alongside comparison objects, where it is especially useful to visualize representations of sequence similarities, like BLAST percentage identity values or e-values.

For the red-blue color scheme, red colors correspond to comparisons that go in the same direction (1), where the blue colors correspond to comparisons that go in the opposite direction (-1).

Author

Lionel Guy

Examples

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

## Color schemes
## Greys
comparisons[[1]]$values <- c(70, 80, 90)
comparisons[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$values,
  color_scheme = "grey")
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons)

## Red-blue
comparisons[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$values,
  direction = comparisons[[1]]$direction,
  color_scheme = "red_blue")
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons)

## Decreasing
comparisons[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$values,
  direction = comparisons[[1]]$direction,
  color_scheme = "red_blue",
  decreasing = TRUE)
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons)

## Range
comparisons[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$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[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$values,
  color_scheme = "grey",
  alpha = 0.8)
comparisons[[2]]$col <- gradient_color_scheme(
  1:nrow(comparisons[[2]]),
  direction = comparisons[[2]]$direction,
  color_scheme = "blue_red")
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons)


comparisons[[1]]$col <- gradient_color_scheme(
  comparisons[[1]]$values,
  color_scheme = "grey",
  alpha = 1)
comparisons[[2]]$col <- gradient_color_scheme(
  1:nrow(comparisons[[2]]),
  direction = comparisons[[2]]$direction,
  color_scheme = "blue_red",
  alpha = 0.2)
plot_gene_map(dna_segs = dna_segs, comparisons = comparisons)