Apply a sequential color scheme to dna_segs and comparisons

Generates and applies a sequential color scheme to a list of dna_seg and comparison objects. It does this by taking the colors that are already there and transferring those over to any features connected to it through the comparisons. For example, if a feature from a single dna_seg has red as its fill attribute, the comparisons that can be linked to this feature will become red as well. This is then followed up by updating any dna_seg features linked to those comparisons, and so on.

Usage

sequential_color_scheme(
  dna_segs,
  comparisons,
  seg_id = "locus_id",
  comparison_id = "auto",
  color_var = "fill",
  default_color = "grey80",
  both_directions = TRUE
)

Arguments

dna_segs: A list of dna_seg objects.
comparisons: A list of comparison objects.
seg_id: The name of a dna_seg column, whose values will be used to make the links to the comparisons.
comparison_id: The shared name of the comparison columns, whose values will be used to make the links to the dna_segs. See details.
color_var: A character string denoting which color attribute to update for the dna_segs, one of: "fill", "col".
default_color: A character string providing a default color, must be either NULL or a valid color. The color given by this argument will be ignored when updating, never overwriting any other color.
both_directions: Logical. If FALSE, the color scheme will be applied sequentially in plotting order, starting from the first dna_seg. When both_directions is TRUE, it will then additionally update each dna_seg and comparison in reverse plotting order.

Value

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

Details

The existing colors from the input dna_seg and comparison objects are transferred over to the next object in the plotting order, with the exception of their default colors, provided by default_color. As comparison objects only have a single color attribute col, those will be updated using the column provided by color_var from the dna_segs, while the dna_segs themselves will be updated using the col column from the comparisons regardless of color_var.

The objects are linked together through shared values. The columns for these shared values are determined by the seg_id and comparison_id arguments, for the dna_segs and comparisons, respectively. comparison_id refers to 2 columns, and defaults to "auto", which will attempt to determine which columns to use automatically. If for example, comparison_id is set as "name", it will look for the "name1" and "name2" columns to match to the seg_id in the dna_segs above, and under it, respectively.

Author

Mike Puijk

Examples

## Prepare dna_seg
names1 <- c("1A", "1B", "1C")
names2 <- c("2A", "2C", "2B")
names3 <- c("3B", "3A", "3C")

## 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),
                               fill = c("darkred", "grey80", "darkblue")))
dna_seg2 <- dna_seg(data.frame(name = names2,
                               start = (1:3) * 3,
                               end = (1:3) * 3 + 2,
                               strand = rep(1, 3),
                               fill = c("grey80", "grey80", "darkgreen")))
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),
                               name1 = c("1A", "1B", "1C"), 
                               name2 = c("2A", "2B", "2C"),
                               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),
                               name1 = c("2A", "2B", "2C"), 
                               name2 = c("3A", "3B", "3C"),
                               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)


## Sequential color scheme without going both directions
full_data <- sequential_color_scheme(list(dna_seg1, dna_seg2, dna_seg3),
                                     comparisons = list(comp1, comp2),
                                     seg_id = "name",
                                     both_directions = FALSE)
plot_gene_map(dna_segs = full_data$dna_segs, 
              comparisons = full_data$comparisons,
              alpha_comparisons = 0.6)


## Sequential color scheme with both directions
full_data <- sequential_color_scheme(list(dna_seg1, dna_seg2, dna_seg3),
                                     comparisons = list(comp1, comp2),
                                     seg_id = "name")
plot_gene_map(dna_segs = full_data$dna_segs, 
              comparisons = full_data$comparisons,
              alpha_comparisons = 0.6)