Create a cell color pallet for plots — create_cell

This function returns a character() vector with valid R colors for a given input character() of unique cell types. These were colors that have been useful in our experience.

create_cell_colors(
  cell_types = c("Astro", "Micro", "Oligo", "OPC", "Inhib", "Excit"),
  pallet = c("classic", "gg", "tableau"),
  split = NA,
  preview = FALSE
)

Arguments

cell_types: A character() vector listing unique cell types.
pallet: Choice of base pallet "classic", "gg", or "tableau".
split: delineating character(1) after which suffixes will be ignored. This is useful for cases when say A.1 and A.2 are both to be considered as cell type A (here split = "\\.").
preview: A logical(1) indicating whether to make a plot to preview the colors.

Value

A named character() vector of R and hex color values compatible with ggplot2:scale_color_manual().

Examples

create_cell_colors(pallet = "classic")
#>     Astro     Micro     Oligo       OPC     Inhib     Excit 
#>       "3"       "4"       "5"       "6" "#E41A1C" "#377EB8" 
create_cell_colors(pallet = "classic", preview = TRUE)

#>     Astro     Micro     Oligo       OPC     Inhib     Excit 
#>       "3"       "4"       "5"       "6" "#E41A1C" "#377EB8" 
create_cell_colors(pallet = "tableau", preview = TRUE)

#>     Astro     Micro     Oligo       OPC     Inhib     Excit 
#> "#1F77B4" "#AEC7E8" "#FF7F0E" "#FFBB78" "#2CA02C" "#98DF8A" 

## Consider A.1 and A.2 as two different cell types (default)
create_cell_colors(
    cell_types = c("A.1", "A.2", "B.1", "C", "D"),
    pallet = "gg",
    preview = TRUE
)

#>       A.1       A.2       B.1         C         D 
#> "#F8766D" "#A3A500" "#00BF7D" "#00B0F6" "#E76BF3" 

## Consider A.1 and A.2 as cell type A by using the "split" argument
create_cell_colors(
    cell_types = c("A.1", "A.2", "B.1", "C"),
    split = "\\.",
    pallet = "gg",
    preview = TRUE
)

#>         A         B         C       A.1       A.2       B.1 
#> "#F8766D" "#00BA38" "#619CFF" "#F8766D" "#FBBAB5" "#00BA38"