Apply a uniform color scheme to dna_segs and comparisons

Generates and applies a uniform color scheme to a list of dna_seg and/ or comparison objects. This is done by generating a set of colors based on a set of unique values taken from a given (shared) column.

Usage

uniform_color_scheme(
  dna_segs = NULL,
  comparisons = NULL,
  id_column,
  ids = NULL,
  cluster_ids = TRUE,
  colors = NULL,
  color_var = "fill",
  alpha_dna_segs = NULL,
  alpha_comparisons = NULL
)

Arguments

dna_segs: A list of dna_seg objects.
comparisons: A list of comparison objects.
id_column: The name of a column, whose unique values will be used to generate a color scheme. Must exist in all provided data sets.
ids: A character vector of values from the id_column to generate colors for. Any values found in the id_column that are not in this set will be ignored.
cluster_ids: Logical. If TRUE, numbered values may be clustered together, sharing a single color. Specifically, it will look for values that end in a number, and when these values are the same once the number is removed, it will cluster them together. For example: "lac_1", "lac-2", and "lac" will all be given the same color. Finally, the value "-" (which is usually the value in the gene column for hypothetical proteins) will also be given its own dedicated color.
colors: Choice of colors to use, can be a palette, or a vector of colors. See details.
color_var: A character string denoting which color attribute to update for the dna_segs, one of: "fill", "col".
alpha_dna_segs: A single numeric value between 0 and 1, or NULL. Determines the transparency applied to the colors used for the dna_segs, 0 being fully transparent, and 1 being fully opaque.
alpha_comparisons: A single numeric value between 0 and 1, or NULL. Determines the transparency applied to the colors used for the comparisons, 0 being fully transparent, and 1 being fully opaque.

Value

If only dna_segs is provided, a list of dna_seg objects.

If only comparisons is provided, a list of comparison objects.

If both dna_segs and comparisons are provided, a list with 2 named elements: dna_segs and comparisons, which are both lists containing the dna_seg and comparison objects, respectively.

Details

The amount of colors generated is equal to the amount of unique values present in the id_column in the data set(s).

The colors argument can be left as NULL, in which case one of 3 different palettes will be used, based on the amount of colors that need to be generated. If not NULL, then colors must be either a character string representing a known palette (see hcl.pals and palette.pals), or a character vector with values that can be recognized as colors (i.e. "red" or "#88CCEE"). If there are not enough colors in this vector, then they will be duplicated and a warning will be given.

Author

Mike Puijk

Examples

## Prepare dna_seg
names1 <- c("A", "B", "C")
names2 <- c("A", "C", "B")
names3 <- c("B", "A", "C")

## Make dna_segs with some alternate colors
dna_seg1 <- dna_seg(data.frame(name = names1,
                               start = (1:3) * 3,
                               end = (1:3) * 3 + 2,
                               strand = rep(1, 3)))
dna_seg2 <- dna_seg(data.frame(name = names2,
                               start = (1:3) * 3,
                               end = (1:3) * 3 + 2,
                               strand = rep(1, 3)))
dna_seg3 <- dna_seg(data.frame(name = names3,
                               start = (1:3) * 3,
                               end = (1:3) * 3 + 2,
                               strand = rep(1, 3)))

## Make comparisons
comp1 <- comparison(data.frame(start1 = c(3, 6, 9), end1 = c(5, 8, 11),
                               start2 = c(3, 9, 6), end2 = c(5, 11, 8),
                               name = c("A", "B", "C"),
                               direction = c(1, 1, 1)))
comp2 <- comparison(data.frame(start1 = c(3, 9, 6), end1 = c(5, 11, 8),
                               start2 = c(6, 3, 9), end2 = c(8, 5, 11),
                               name = c("A", "B", "C"),
                               direction = c(1, 1, 1)))

## Before adding a color scheme
plot_gene_map(dna_segs = list(dna_seg1, dna_seg2, dna_seg3), 
              comparisons = list(comp1, comp2),
              alpha_comparisons = 0.6)


## Apply uniform color scheme
full_data <- uniform_color_scheme(list(dna_seg1, dna_seg2, dna_seg3),
                                  comparisons = list(comp1, comp2),
                                  id_column = "name")
plot_gene_map(dna_segs = full_data$dna_segs, 
              comparisons = full_data$comparisons,
              alpha_comparisons = 0.6)


## Use ids and colors to specify the values and colors to use
full_data <- uniform_color_scheme(list(dna_seg1, dna_seg2, dna_seg3),
                                  comparisons = list(comp1, comp2),
                                  id_column = "name",
                                  ids = c("A", "C"),
                                  colors = c("purple", "#F8A19F"))
plot_gene_map(dna_segs = full_data$dna_segs, 
              comparisons = full_data$comparisons,
              alpha_comparisons = 0.6)