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296 lines (261 loc) · 18.6 KB
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##########################################
### parameters used for making 3D UMAP ###
##########################################
t1 = list(family = 'Helvetica',
size = 25,
color = "black")
t2 = list(family = 'Helvetica',
size = 15,
color = "grey")
####################################
### major trajectory color plate ###
####################################
major_trajectory_color_plate = c("Neuroectoderm_and_glia" = "#f96100",
"Intermediate_neuronal_progenitors" = "#2e0ab7",
"Eye_and_other" = "#00d450",
"Ependymal_cells" = "#b75bff",
"CNS_neurons" = "#e5c000",
"Mesoderm" = "#bb46c5",
"Definitive_erythroid" = "#dc453e",
"Epithelial_cells" = "#af9fb6",
"Endothelium" = "#00a34e",
"Muscle_cells" = "#ffa1f5",
"Hepatocytes" = "#185700",
"White_blood_cells" = "#7ca0ff",
"Neural_crest_PNS_glia" = "#fff167",
"Adipocytes" = "#7f3e39",
"Primitive_erythroid" = "#ffa9a1",
"Neural_crest_PNS_neurons" = "#b5ce92",
"T_cells" = "#ff9d47",
"Lung_and_airway" = "#02b0d1",
"Intestine" = "#ff007a",
"B_cells" = "#01b7a6",
"Olfactory_sensory_neurons" = "#e6230b",
"Cardiomyocytes" = "#643e8c",
"Oligodendrocytes" = "#916e00",
"Mast_cells" = "#005361",
"Megakaryocytes" = "#3f283d",
"Testis_and_adrenal" = "#585d3b")
######################################
### Timepoints between E8.5 and P0 ###
######################################
day_color_plate = c("E8.0" = "#5E4FA2", "E8.25" = "#545BA8", "E8.5" = "#4A68AE", "E8.75" = "#4075B4",
"E9.0" = "#3682BA", "E9.25" = "#398FB9", "E9.5" = "#449DB4", "E9.75" = "#50AAAE",
"E10.0" = "#5CB7A9", "E10.25" = "#69C3A4", "E10.5" = "#78C9A4", "E10.75" = "#88CFA4",
"E11.0" = "#98D5A4", "E11.25" = "#A7DBA4", "E11.5" = "#B5E1A1", "E11.75" = "#C3E69F",
"E12.0" = "#D0EC9C", "E12.25" = "#DDF199", "E12.5" = "#E8F59B", "E12.75" = "#EDF8A4",
"E13.0" = "#F3FAAD", "E13.25" = "#F9FCB6", "E13.5" = "#FFFFBF", "E13.75" = "#FEF7B3",
"E14.0" = "#FEF0A7", "E14.25" = "#FEE99B", "E14.333" ="#FEE28F", "E14.75" = "#FDD985",
"E15.0" = "#FDCD7B", "E15.25" = "#FDC272", "E15.5" = "#FDB768", "E15.75" = "#FCAB5F",
"E16.0" = "#FA9C58", "E16.25" = "#F88D52", "E16.5" = "#F67E4B", "E16.75" = "#F46F44",
"E17.0" = "#EE6445", "E17.25" = "#E75947", "E17.5" = "#E04F4A", "E17.75" = "#D9444D",
"E18.0" = "#CF384D", "E18.25" = "#C32A4A", "E18.5" = "#B71C47", "E18.75" = "#AA0E44",
"P0" = "#9E0142")
#################################
### Somite counts color plate ###
#################################
somite_color_plate = rev(c("#fde725", "#eae51a", "#d5e21a", "#c0df25", "#a8db34",
"#93d741", "#7fd34e", "#6ccd5a", "#58c765", "#48c16e",
"#3aba76", "#2eb37c", "#25ab82", "#20a386", "#1e9c89",
"#1f948c", "#228c8d", "#25848e", "#287d8e", "#2b758e",
"#2e6d8e", "#32658e", "#365d8d", "#3a548c", "#3e4a89",
"#424186", "#453882", "#472e7c", "#482374", "#48186a",
"#470d60", "#440154"))
names(somite_color_plate) = paste0(c(0, 2:12, 14:18, 20:34), " somites")
####################################
### Posterior embryo color plate ###
####################################
posterior_embryo_color_plate = c("Notochord" = "#1F77B4",
"Nodal cilia" = "#FF7F0E",
"NMPs and spinal cord progenitors" = "#2CA02C",
"Gut" = "#D62728",
"Mesodermal progenitors (Tbx6+)" = "#9467BD")
#########################
### renal color plate ###
#########################
renal_color_plate = c("Posterior intermediate mesoderm" = "#A6CEE3",
"Anterior intermediate mesoderm" = "#1F78B4",
"Ureteric bud" = "#B2DF8A",
"Collecting duct intercalated cells" = "#33A02C",
"Collecting duct principal cells" = "#FB9A99",
"Metanephric mesenchyme" = "#E31A1C",
"Nephron progenitors" = "#FDBF6F",
"Podocytes" = "#FF7F00",
"Proximal tubule cells" = "#CAB2D6",
"Ascending loop of Henle" = "#6A3D9A",
"Distal convoluted tubule" = "#FFFF99",
"Connecting tubule" = "#B15928")
##########################################
### lateral plate mesoderm color plate ###
##########################################
LPM_color_plate = c("Splanchnic mesoderm" = "#ca47cc",
"Lung mesenchyme" = "#6dd251",
"Hepatic mesenchyme" = "#663fc6",
"Renal stromal cells" = "#f8f434",
"Cardiopharyngeal mesoderm" = "#3f2b71",
"Vascular smooth muscle cells" = "#c1bf5a",
"Vascular smooth muscle cells (Pparg+)" = "#9f7ada",
"Meninges" = "#6ad39e",
"Airway smooth muscle cells" = "#dc4989",
"Amniotic mesoderm" = "#587f3a",
"Allantois" = "#8f3e7f",
"Extraembryonic mesoderm" = "#d58d40",
"Somatic mesoderm" = "#7d9cd9",
"Renal pericytes and mesangial cells" = "#d94e38",
"Gut mesenchyme" = "#79bec6",
"Foregut mesenchyme" = "#983b40",
"Gastrointestinal smooth muscle cells" = "#7f5d35",
"Gonad progenitor cells" = "#42222e",
"Sertoli cells" = "#d399af",
"Granulosa cells" = "#516aca",
"Proepicardium" = "#5b6180",
"Mesothelial cells" = "#3a5440")
LPM_E85_color_plate = c("Anterior intermediate mesoderm" = "#1F78B4",
"First heart field" = "#d85091",
"Lateral plate and intermediate mesoderm" = "#7d5a3b",
"Mesodermal progenitors (Tbx6+)" = "#38503a",
"Posterior intermediate mesoderm" = "#A6CEE3",
"Second heart field" = "#3d2130",
"LPM:Allantois" = "#8f3e7f",
"LPM:Amniotic mesoderm" = "#587f3a",
"LPM:Cardiopharyngeal mesoderm" = "#3f2b71",
"LPM:Extraembryonic mesoderm" = "#d58d40",
"LPM:Foregut mesenchyme" = "#983b40",
"LPM:Gut mesenchyme" = "#79bec6",
"LPM:Hepatic mesenchyme" = "#663fc6",
"LPM:Proepicardium" = "#5b6180",
"LPM:Renal pericytes and mesangial cells" = "#d94e38",
"LPM:Somatic mesoderm" = "#7d9cd9",
"LPM:Splanchnic mesoderm" = "#ca47cc",
"NMPs and spinal cord progenitors" = "#cb566d",
"LPM:Gonad progenitor cells" = "#42222e",
"LPM:Lung mesenchyme" = "#6dd251",
"LPM:Meninges" = "#6ad39e",
"LPM:Vascular smooth muscle cells" = "#c1bf5a",
"LPM:Mesothelial cells" = "#3a5440")
#######################
### eye color plate ###
#######################
eye_color_plate = c("Eye field" = '#6d8840',
"Retinal pigment cells" = '#c95493',
"Naive retinal progenitor cells" = "#A6CEE3",
"Retinal progenitor cells" = "#1F78B4",
"Bipolar precursor cells" = "#B2DF8A",
"Ciliary margin cells" = "#33A02C",
"Photoreceptor precursor cells" = "#FB9A99",
"Cone precursor cells" = "#E31A1C",
"Rod precursor cells" = "#FDBF6F",
"Retinal ganglion cells" = "#FF7F00",
"PV-containing retinal ganglion cells" = "#CAB2D6",
"Amacrine/Horizontal precursor cells" = "#6A3D9A",
"Amacrine cells" = "#FFFF99",
"Horizontal cells" = "#B15928",
"Cholinergic amacrine cells" = "#808080")
#################################
### neuroectoderm color plate ###
#################################
neuroectoderm_color_plate = c("Spinal dI1 interneurons" = '#636EFA',
"Spinal dI2 interneurons" = '#EF553B',
"Spinal dI3 interneurons" = '#00CC96',
"Spinal dI4 interneurons" = '#AB63FA',
"Spinal dI5 interneurons" = '#FFA15A',
"Spinal dI6 interneurons" = '#19D3F3',
"Spinal V0 interneurons" = '#FF6692',
"Spinal V1 interneurons" = '#B6E880',
"Spinal V2a interneurons" = '#FECB52',
"Spinal V2b interneurons" = '#1F77B4',
"Spinal V3 interneurons" = '#FF7F0E',
"Di/mesencephalon glutamatergic neurons" = '#2CA02C',
"Striatal projection neurons" = '#9467BD',
"Precerebellar neurons" = '#8C564B',
"Di/mesencephalon GABAergic neurons" = '#E377C2',
"Hypothalamic Sim1 neurons" = '#7F7F7F',
"Midbrain dopaminergic neurons" = '#BCBD22',
"Spinal cord motor neuron progenitors" = '#17BECF',
"Spinal cord motor neurons" = "#17BECF",
"Anterior floor plate" = "#9a632b",
"Anterior roof plate" = "#b1c4d9",
"Diencephalon" = "#9e3136",
"Dorsal telencephalon" = "#93d6b6",
"Hindbrain" = "#8f366c",
"Hypothalamus" = "#848b38",
"Hypothalamus (Sim1+)" = "#52288d",
"Midbrain" = "#d3c398",
"Midbrain-hindbrain boundary" = "#3d2945",
"Floorplate and p3 domain" = "#b898c9",
"Posterior roof plate" = "#363d27",
"Spinal cord/r7/r8" = "#467d4e",
"Telencephalon" = "#d98f90",
"Astrocytes" = "#504d84",
"Cajal-Retzius cells" = "#cfd98e",
"Choroid plexus" = "#692135",
"Cranial motor neurons" = "#65e3be",
"Eye field" = "#c15a34",
"GABAergic cortical interneurons" = "#e8afd6",
"Intermediate progenitors" = "#45251f",
"Neural progenitor cells (Neurod1+)" = "#d7c1b7",
"Neurons (Slc17a8+)" = "#437a7d",
"Thalamic neuronal precursors" = "#5f5b28")
astrocytes_color_plate = c("VA1 astrocytes" = "#9ac25e",
"VA2 astrocytes" = "#b35948",
"VA3 astrocytes" = "#b98b3a",
"Anterior astrocytes" = "#8d50a9")
neuron_day_color_plate = rev(c("#fcffa4", "#f2ea69", "#f9cb35", "#fcac11", "#f98e09",
"#f1731d", "#e45a31", "#d24644", "#bc3754", "#a32c61",
"#8a226a", "#71196e", "#57106e", "#3d0965", "#210c4a", "#0b0724", "#000004"))
names(neuron_day_color_plate) = c("E8.75", "E9.0", "E9.25", "E9.5", "E9.75", "E10.0", "E10.25",
"E10.5", "E10.75", "E11.0", "E11.25", "E11.5", "E11.75", "E12.0",
"E12.25", "E12.5", "E12.75")
################################
### Birth-series color plate ###
################################
birth_color_plate = c("E18.75" = "#7aa457",
"P0" = "#cb6a49",
"Csection_0m" = "#0d0887",
"Csection_20m" = "#7e03a8",
"Csection_40m" = "#cc4778",
"Csection_60m" = "#f89540",
"Csection_80m" = "#f0f921",
"NatBirth" = "#02b0d1",
"NatBirth_rep1" = "#02b0d1",
"NatBirth_rep2" = "#02b0d1",
"NatBirth_rep3" = "#02b0d1")
######################################
### Re-annotation P-S + E8.5b data ###
######################################
gastrulation_color_plate = c("Allantois" = "#8f3e7f",
"Amniotic mesoderm" = "#587f3a",
"Extraembryonic mesoderm" = "#d58d40",
"Gut mesenchyme" = "#79bec6",
"Hindbrain" = "#8f366c",
"Primitive erythroid cells" = "#c96d44",
"Blood progenitors" = "#5d69d7",
"Cardiopharyngeal mesoderm" = "#e68028",
"Definitive ectoderm" = "#4e7ac1",
"Embryonic visceral endoderm" = "#d2482a",
"Epiblast" = "#58abe3",
"Floor plate" = "#d13e4b",
"Gut" = "#54c465",
"Hematoendothelial progenitors" = "#c843ae",
"Intermediate mesoderm" = "#77b635",
"Midbrain" = "#d77fdc",
"Neural crest" = "#d3a52d",
"Paraxial mesoderm (Tbx6-)" = "#9652c6",
"Parietal endoderm" = "#a8ad38",
"Primitive streak" = "#7d5fa4",
"Spinal cord" = "#388a35",
"Amniotic ectoderm" = "#dc4074",
"Anterior primitive streak" = "#5cbf8c",
"Cardiogenic mesoderm" = "#d64694",
"CLE and NMPs" = "#41bcb3",
"Definitive endoderm" = "#994f2d",
"Endothelium" = "#af99e2",
"Extraembryonic ectoderm" = "#956f2c",
"Extraembryonic visceral endoderm" = "#ae5c82",
"Forebrain" = "#9cb36a",
"Lateral plate mesoderm" = "#e389b6",
"Nascent mesoderm" = "#318766",
"Notochord" = "#e48380",
"Paraxial mesoderm (Tbx6+)" = "#737129",
"Primordial germ cells" = "#ac4b55",
"Surface ectoderm" = "#cea365")