Color cell types

color_cell_types.R

  
 get_cell_type_color = function(cell_type_vector){
  
  cell_type_vector |> 
    enframe(value = "harmonised_cell_type") |> 
    left_join(
      tribble(
        ~harmonised_cell_type, ~palette,
        
        # B
        'b memory', "Purples",
        'b naive', "Purples",
        'plasma', "Purples",
        'pdc', "Purples",
        
        # Mono
        'cd14 mono',  "Blues", 
        'cd16 mono', "Blues", 
        'cdc', "Blues", 
        'macrophage', "Blues", 
        
        # T
        'tregs', "Reds",
        'treg', "Reds",
        'cd4',  "Reds",
        'cd8',  "Reds",
        'cd4 naive',  "Reds",
        'cd4 tcm', "Reds",
        'cd4 tem',  "Reds",
        "cd4 fh" ,  "Reds",
        "cd4 th1" ,  "Reds",
        "cd4 th1/th17" ,  "Reds",
        "cd4 th17" ,  "Reds",
        "cd4 th2",  "Reds",
        "cd4 term eff", "Reds",
        "terminal effector cd4 t", "Reds",
        
        # T cytotoxic
        'cd8 naive',  "Oranges",
        'cd8 tcm',  "Oranges",
        'cd8 tem', "Oranges",
        'mait',  "Oranges",
        'tgd',  "Oranges",
        
        # Other
        'nk', "Greens",
        'ilc', "Greens",
        
        'non_immune', "Greys",
        'stem', "Greys",
        'mast', "Greys",
        NA, "Greys"
      ),
      by = join_by(harmonised_cell_type)
    ) |> 
    tidyr::replace_na(list(palette = "Greys")) |> 
    nest(data = -palette) |>
    mutate(color = map2(palette,  data, ~ RColorBrewer::brewer.pal(max(nrow(.y), 3), .x)[1:nrow(.y)] )) |>
    unnest(c(data, color)) |>
    dplyr::select(harmonised_cell_type, color ) |>
    deframe()
  
}

  
  
  color_array =
  tibble(
    harmonised_cell_type = c('b memory', 'b naive', 'plasma', 'cd14 mono', 'cd16 mono', 'treg', 'mait', 'tgd', 'cd4', 'cd8', 'cd4 naive', 'cd4 tcm', 'cd4 tem', 'cd8 naive', 'cd8 tcm', 'cd8 tem', 'cdc', 'immune_unclassified', 'macrophage', 'mast', 'nk', 'ilc', 'non_immune', 'pdc', 'stem', 'treg', NA)
  ) |>
    mutate(palette = c("Purples", "Purples", "Purples", "Blues", "Blues", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Reds", "Blues", "Greys", "Blues", "Greys", "Greens", "Greens", "Greys", "Blues", "Greys", "Reds", "Greys")) |>
    nest(data = -palette) |>
    mutate(color = map2(palette,  data, ~ RColorBrewer::brewer.pal(max(nrow(.y), 3), .x)[1:nrow(.y)] )) |>
    unnest(c(data, color)) |>
  dplyr::select(harmonised_cell_type, color ) |>
  deframe()