apply_color_scheme: Apply a color scheme

In genoPlotR: Plot Publication-Grade Gene and Genome Maps

Description

Apply a color scheme to a numeric vector, eventually taking the direction into account.

Usage

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.

Value

A character vector of same length as x, representing colors.

Author(s)

Lionel Guy

References

Artemis Comparison Tool, https://www.sanger.ac.uk/tool/artemis-comparison-tool-act/

See Also

comparison

Examples

## 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)

Example output

Loading required package: ade4
Loading required package: grid

genoPlotR documentation built on Jan. 7, 2021, 5:08 p.m.