given a nucleotide sequence, generate an index-color string recognized by forna

forna_colors.R

# requires the native pipe from R >= 4.1
## maps each base to a particular color
## colors can be named or hex values
## outputs a format recognized by the forna webapp's custom color editor
## http://rna.tbi.univie.ac.at/forna/forna.html

forna_colors <- function(sequence, colormap) {
  inseq <- gsub(x = strsplit(toupper(as.character(sequence)),split="")[[1]],
                pattern="T",
                replacement="U")
  index <- paste0(1:length(inseq),":")
  c(rbind(index,inseq)) |>
    gsub(pattern = names(colormap[1]), replacement = paste0(tolower(colormap[1])," ")) |>
    gsub(pattern = names(colormap[2]), replacement = paste0(tolower(colormap[2])," ")) |>
    gsub(pattern = names(colormap[3]), replacement = paste0(tolower(colormap[3])," ")) |>
    gsub(pattern = names(colormap[4]), replacement = paste0(tolower(colormap[4])," ")) |>
    paste0(collapse = "") |> trimws() |> noquote()
}

# example
seq <- "GGCCCCATGGTCAAGCGGTTAAGACATCGCCCTTTCACGGCGGTAACACGGGTTCAAATCCCGTTGGGGTCA"
colors <- c(A = "yellow", G = "red", C = "green", U = "blue")
colors_hex <- c(A = "#5BB57E", G = "#F8C966", C = "#668DB7", U = "#E26674") 
forna_colors(seq, colors)
forna_colors(seq, colors_hex)