R/plot_utils.R

In dkeitley/scrabbitr: Single-cell RNA-seq analysis of rabbit gastrulation

celltype_colours <- c(
                      # Existing mouse colours
                      "Definitive Endoderm" = "#EF4E22",
                      "Gut endoderm" = "#EF5A9D",
                      "Megakaryocytes" = "#ac0404",
                      "Visceral YS endoderm" = "#9d506e",
                      "Parietal YS endoderm" = "#1A1A1A",
                      "Epiblast" = "#635547",
                      "Primitive Streak" = "#DABE99",
                      "Caudal epiblast" = "#9E6762",
                      "PGC" = "#FACB12",
                      "Anterior Primitive Streak" = "#C19F70",
                      "Node"="#153B3D",
                      "Notochord" = "#0F4A9C",
                      "Gut tube" = "#F063A4",
                      "Hindgut" = "#F397C0",
                      "Midgut"  = "#FF00B2",
                      "Foregut" = "#FFB7FF",
                      "Pharyngeal endoderm"="#95E1FF",
                      "Thyroid primordium"="#97BAD3",
                      "Nephron progenitors"="#E85639",
                      "Nascent mesoderm" = "#C594BF",
                      "Intermediate mesoderm" = "#139992",
                      "Caudal mesoderm" = "#3F84AA",
                      "Lateral plate mesoderm" = "#F9DFE6",
                      "Limb mesoderm" = "#E35F82",
                      "Forelimb" = "#D02D75",
                      "Presomitic mesoderm"="#5581CA",#"#0000ff",#fc
                      "Somitic mesoderm" = "#005579",
                      "Posterior somitic tissues" = "#5ADBE4",#"#40e0d0",#turquoise
                      "Paraxial mesoderm" = "#8DB5CE",
                      "Cranial mesoderm" = "#456722",#"#006400",#darkgreen
                      "Anterior somitic tissues"= "#D5E839",
                      "Sclerotome" = "#E3CB3A",#"#ffff00",#yellow
                      "Dermomyotome" = "#00BFC4",#"#a52a2a",#brown
                      "Pharyngeal mesoderm" = "#C9EBFB",
                      "Cardiopharyngeal progenitors" = "#556789",
                      "Anterior cardiopharyngeal progenitors"="#683ED8",
                      "Allantois" = "#532C8A",
                      "Mesenchyme" = "#CC7818",
                      "Mesothelium" = "#FF7F9C",
                      "Epicardium"="#F79083",
                      "EPDC" = "#FF487D",
                      "Cardiopharyngeal progenitors FHF"="#D780B0",
                      "Cardiomyocytes FHF 1"="#A64D7E",
                      "Cardiomyocytes FHF 2"="#B51D8D",
                      "Cardiopharyngeal progenitors SHF"="#4B7193",
                      "Cardiomyocytes SHF 1"="#5D70DC",
                      "Cardiomyocytes SHF 2"="#332C6C",
                      "Haematoendothelial progenitors" = "#FBBE92",
                      "Blood progenitors" = "#6C4B4C",
                      "Erythroid" = "#C72228",
                      "Erythroid/Masked"="#FF0000",
                      "MEP"="#F15B32",
                      "EMP"="#7C2A47",
                      "YS endothelium"="#FF891C",
                      "Mesothelium-endothelium/Masked"="#0000FF",
                      "Allantois endothelium"="#2F4A60",
                      "Embryo proper endothelium"="#90E3BF",
                      "Venous endothelium"="#BD3400",
                      "Endocardium"="#9D0049",
                      "NMPs/Mesoderm-biased" = "#89C1F5",
                      "NMPs" = "#8EC792",
                      "Ectoderm" = "#FF675C",
                      "Optic vesicle" = "#BD7300",
                      "Ventral forebrain progenitors"="#A0B689",
                      "Early dorsal forebrain progenitors"="#0F8073",
                      "Late dorsal forebrain progenitors"="#7A9941",
                      "Midbrain/Hindbrain boundary"="#8AB3B5",
                      "Midbrain progenitors"="#9BF981",
                      "Dorsal midbrain neurons"="#12ED4C",
                      "Ventral hindbrain progenitors"="#7E907A",
                      "Dorsal hindbrain progenitors"="#2C6521",
                      "Hindbrain floor plate"="#BF9DA8",
                      "Hindbrain neural progenitors"="#59B545",
                      "Neural tube"="#233629",
                      "Migratory neural crest"="#4A6798",
                      "Branchial arch neural crest"="#BD84B0",
                      "Frontonasal mesenchyme"="#D3B1B1",
                      "Spinal cord progenitors"="#6B2035",
                      "Dorsal spinal cord progenitors"="#E273D6",
                      "Non-neural ectoderm 1" = "#F7F79E",
                      "Non-neural ectoderm 2" = "#FCFF00",
                      "Non-neural ectoderm 3" = "#FFF335",
                      "Non-neural ectoderm 4" = "#FFD731",
                      "Non-neural ectoderm 5" = "#DBB400",
                      "Placodal ectoderm"="#FF5C00",
                      "Otic placode"="#F1A262",
                      "Otic neural progenitors"="#00B000",
                      "Visceral endoderm" = "#F6BFCB",
                      "ExE endoderm" = "#7F6874",
                      "ExE ectoderm" = "#989898",
                      "Parietal endoderm" = "#1A1A1A",
                      "Blood progenitors 1" = "#f9decf",
                      "Blood progenitors 2" = "#c9a997",
                      "Caudal mesoderm" = "#3F84AA",
                      "Endothelium" = "#ff891c",
                      "Megakariocytes" = "#ac0404",
                      "Caudal neurectoderm" = "#354E23",
                      "Unknown"="#000000",
                      "Other"="#000000",

                      # Additional rabbit colours
                      'Cranial neural crest' = "#BD84B0",
                      "Spinal cord"= "#6B2035",
                      "Differentiating neurons"="#12ED4C",
                      "Floor plate" = "#BF9DA8",
                      "Hypoblast"="#7F6874",
                      'Forebrain'= "#FF4A46",
                      'Midbrain'= "#0000A6",
                      'Hindbrain'="#63FFAC",
                      'Roof plate'= "#772600",
                      'Visceral YS endoderm 2'= "#5B4534",
                      'Amnion 1'= '#549E79',
                      'Amnion 2'= '#f0e400',
                      'Amnion 3'= '#dea93c',
                      'Trophoblast'= '#989898',
                      'Cytotrophoblast'= '#46c5bf',
                      'Syncytiotrophoblast progenitors'= '#7766db',
                      "Syncytiotrophoblast" = '#7295e2',
                      'SCT progenitors' = '#7766db',
                      'Early SCT' = '#7295e2'
)


stage_colours <- c(
  "E6.5" = "#723957",
  "E6.75" = "#823C3C",
  "E7.0" ="#93502D",
  "E7.25"="#A9742E",
  "E7.5"="#C3A34B",
  "E7.75"="#D5CE81",
  "E8.0"="#CBE0B1",
  "E8.25"="#A4D8CA",
  "E8.5"="#73BACC",
  "E8.75"="#5394BF",
  "E9.0"="#506BA4",
  "E9.25"="#61497D",
  "E9.5"="#723959",

  #Rabbit
  "GD7" = "#93502D",
  "GD8" = "#CBE0B1",
  "GD9" = "#506BA4"

)


godsnot_102 <- c(
  "#FFFF00",
  "#1CE6FF",
  "#FF34FF",
  "#FF4A46",
  "#008941",
  "#006FA6",
  "#A30059",
  "#FFDBE5",
  "#7A4900",
  "#0000A6",
  "#63FFAC",
  "#B79762",
  "#004D43",
  "#8FB0FF",
  "#997D87",
  "#5A0007",
  "#809693",
  "#6A3A4C",
  "#1B4400",
  "#4FC601",
  "#3B5DFF",
  "#4A3B53",
  "#FF2F80",
  "#61615A",
  "#BA0900",
  "#6B7900",
  "#00C2A0",
  "#FFAA92",
  "#FF90C9",
  "#B903AA",
  "#D16100",
  "#DDEFFF",
  "#000035",
  "#7B4F4B",
  "#A1C299",
  "#300018",
  "#0AA6D8",
  "#013349",
  "#00846F",
  "#372101",
  "#FFB500",
  "#C2FFED",
  "#A079BF",
  "#CC0744",
  "#C0B9B2",
  "#C2FF99",
  "#001E09",
  "#00489C",
  "#6F0062",
  "#0CBD66",
  "#EEC3FF",
  "#456D75",
  "#B77B68",
  "#7A87A1",
  "#788D66",
  "#885578",
  "#FAD09F",
  "#FF8A9A",
  "#D157A0",
  "#BEC459",
  "#456648",
  "#0086ED",
  "#886F4C",
  "#34362D",
  "#B4A8BD",
  "#00A6AA",
  "#452C2C",
  "#636375",
  "#A3C8C9",
  "#FF913F",
  "#938A81",
  "#575329",
  "#00FECF",
  "#B05B6F",
  "#8CD0FF",
  "#3B9700",
  "#04F757",
  "#C8A1A1",
  "#1E6E00",
  "#7900D7",
  "#A77500",
  "#6367A9",
  "#A05837",
  "#6B002C",
  "#772600",
  "#D790FF",
  "#9B9700",
  "#549E79",
  "#FFF69F",
  "#201625",
  "#72418F",
  "#BC23FF",
  "#99ADC0",
  "#3A2465",
  "#922329",
  "#5B4534",
  "#FDE8DC",
  "#404E55",
  "#0089A3",
  "#CB7E98",
  "#A4E804",
  "#324E72")


#' @export
getCelltypeColours <- function() {
  return(celltype_colours)
}

#' @export
getStageColours <- function() {
  return(stage_colours)
}

#' @export
getDiscreteColours <- function(x) {
  if(class(x)=="int") return(godsnot_102[1:x])
  else if (length(x)>1) {
    pal <- godsnot_102[1:length(x)]
    names(pal) <- names(x)
    return(pal)
  }
}