inst/scripts/make-annotation-colors.R

In massonix/HCATonsilData: Provide programmatic access to the tonsil cell atlas datasets

# This script creates the colors colors_20230508, so that we can recreate
# UMAPs and violin plots using the same color palettes used in the paper.

colors_20230508 <- list(
  level_1 = c(
    "NBC_MBC" = "#a6cee3",
    "GCBC" = "#398D9F",
    "PC" = "#032872",
    "CD4_T" = "#a50000",
    "Cytotoxic" = "#67253a",
    "myeloid" = "#6ac087",
    "FDC" = "#d5ff00",
    "PDC" = "#f032e6",
    "epithelial" = "#ffdc9f",
    "preBC" = "#45d7c7",
    "preTC" = "#e87281"
  ),
  "NBC-MBC" = c(
    "NBC" = "#dbeef2",
    "NBC early activation" = "#95cce0",
    "NBC IFN-activated" = "#4d828c",
    "NBC CD229+" = "#8a73ae",
    "Early GC-commited NBC" = "#74c9b8",
    "GC-commited NBC" = "#6dcbb4",
    "preGC" = "#6ebf90",
    "Proliferative NBC" = "#205b69",
    "GC DZ Noproli" = "#558e1b",
    "Early MBC" = "#ebe2c3",
    "ncsMBC" = "#dccb9b",
    "ncsMBC FCRL4/5+" = "#bca041",
    "csMBC" = "#6f663a",
    "csMBC FCRL4/5+" = "#a29158",
    "MBC FCRL5+" = "#332d1b"
  ),
  "GCBC" = c(
    "DZ early Sphase"= "#036ebf",
    "DZ late Sphase" = "#004f89",
    "DZ early G2Mphase" = "#6f65a1",
    "DZ late G2Mphase" = "#867fa8",
    "DZ cell cycle exit" = "#2e2d4c",
    "DZ non proliferative" = "#336103",
    "DZ_LZ transition" = "#d0efa1",
    "LZ" = "#fbf397",
    "LZ_DZ reentry commitment" = "#e1efef",
    "LZ proliferative" = "#97d1f8",
    "LZ_DZ transition" = "#4eb0f9",
    "Precursor MBCs" = "#c4b771",
    "Reactivated proliferative MBCs" = "#574b2e",
    "PC committed Light Zone GCBC" = "#fccac3"
  ),
  "PC" = c(
    "Dark Zone GCBC" = "#76797e",             
    "DZ migratory PC precursor" = "#d74403",
    "Light Zone GCBC" = "#b8bac1",
    "PC committed Light Zone GCBC" = "#fccec4",
    "Early PC precursor" = "#fd887d",
    "PB committed early PC precursor" = "#eebecb",
    "Transitional PB" = "#e57d95",
    "PB" = "#c24667",           
    "IgG+ PC precursor" = "#a3e0ee",
    "preMature IgG+ PC" = "#0a8fc8",
    "Mature IgG+ PC" = "#304074",
    "MBC derived IgG+ PC" = "#546a9d",
    "Mature IgA+ PC" = "#4a322e",
    "MBC derived IgA+ PC" = "#866a5a",
    "csMBC" = "#035e6f",
    "MBC derived early PC precursor" = "#418b9d",
    "MBC derived PC precursor" = "#96c2cf",
    "IgM+ early PC precursor" = "#62b160",     
    "IgM+ PC precursor" = "#1a8e18",
    "preMature IgM+ PC" = "#016400",
    "Mature IgM+ PC" = "#013701",
    "Short lived IgM+ PC" = "#92cc92",
    "IgD PC precursor" = "#f3ddc2"
  ),
  "CD4-T" = c(
    "Naive" = "gray88",
    "CM Pre-non-Tfh" = "gray71",
    "CM PreTfh" = "gray59",
    "Tfh T:B border" = "#67a9cf",
    "Tfh-LZ-GC" = "#3690c0",
    "GC-Tfh-SAP" = "#02818a",
    "GC-Tfh-OX40"= "#016c59",
    "Tfh-Mem" = "#014636",
    "T-Trans-Mem" = "#fd8d3c",
    "T-Eff-Mem" = "#e31a1c",
    "T-helper" = "#800026",
    "Eff-Tregs" = "#df65b0",
    "Eff-Tregs-IL32" = "#e7298a",
    "Tfr" = "#ce1256",
    "cycling T" = "#e9001b"
  ),
  "Cytotoxic" = c(
    "Naive CD8 T" = "#ffb6c1",
    "SCM CD8 T" = "#ffc4a6",
    "CM CD8 T" = "#e46c70",
    "RM CD8 T" = "#ce262f",
    "RM CD8 activated T" = "#862222",
    "CD8 Tf" = "#74b2d0",
    "DC recruiters CD8 T" = "#9E8073", 
    "IFN+ CD8 T" = "#441815",
    "EM CD8 T" = "#E58F47",
    "ZNF683+ CD8 T" = "#a2c8c7",
    "non-Vδ2+ γδ T" = "#5ea19e",
    "MAIT/Vδ2+ γδ T" = "#008080",
    "CD16-CD56+ NK" = "#a19d41",
    "CD16-CD5dim- NK" = "#fcf75e",
    "CD16+CD56dim NK" = "#cec94f",
    "ILC1" = "#80eda8",
    "NKp44+ ILC3" = "#6ac18a",
    "NKp44- ILC3" = "#55976d",
    "DN"= "#003b59" 
  ),
  "myeloid" = c(
    "DC1 precursor" = "#ff99d6",
    "DC1 mature" = "#bf408c",
    "DC2" = "#f99fa7",
    "DC3" = "#e06c6c",
    "DC4" = "#8f523d",
    "DC5" = "#d73919",
    "IL7R DC" = "#e1b40e",
    "aDC1" = "#e2f155",
    "aDC2" = "#b4d84b",
    "aDC3" = "#6ead34",
    "M1 Macrophages" = "#3f56ca",
    "Monocytes" = "#cd87de",
    "Mast" = "#825e7b",
    "Neutrophils" = "#aa7c60",
    "Cycling" = "gray",
    "MMP Slan-like" = "#91f8ca",
    "C1Q Slan-like" = "#68cde8",
    "SELENOP Slan-like" = "#519bdb",
    "ITGAX Slan-like" = "#7ef1eb"
  ),
  "FDC" = c(
    "FDC" = "#632c63",
    "cycling FDC" = "#cc66cc",
    "CD14+CD55+ FDC" = "#e4624e",
    "COL27A1+ FDC" = "#92e8df",
    "FRC" = "yellow3",
    "MRC" = "limegreen",
    "unknown" = "#999999"
  ),
  "epithelial" = c(
    "Basal cells" = "#1b9e77",
    "VEGFA+" = "#d95f02",
    "Surface epithelium" = "#7570b3",
    "Outer surface" = "#e7298a",
    "Crypt" = "#66a61e",
    "FDCSP epithelium" = "#e6ab02"
  ),
  "PDC" = c(
    "PDC" = "#f032e6",
    "IFN1+ PDC" = "#510791"
  )
)

save(colors_20230508, file = here::here("data/colors_20230508.RData"))