scripts/figures/palette.py

"""canonical class -> color mapping shared across every panda figure.

related classes share hue families (fibroblasts red, keratinocytes orange,
melanocyte lineage purple, endothelial teal, immune yellow, etc.). every
figure imports CLASS_COLORS[cls] so class X gets the same color everywhere.
"""

# skin (13 classes)
_SKIN = {
    "basal-IFE":            "#e07b39",  # keratinocyte orange
    "spinous":              "#c94f21",
    "granular":             "#a53818",
    "HF-placode":           "#8b4513",  # hair follicle brown
    "HF-ORS":               "#c68e4b",
    "sebaceous":            "#bfa970",
    "fibroblast-papillary": "#d94848",  # fibroblast reds
    "fibroblast-reticular": "#8f1e1e",
    "endothelial":          "#2e8b8b",  # vascular teal
    "immune":               "#d1c02b",  # immune yellow
    "melanoblast":          "#6a5acd",  # melanocyte purples
    "melanocyte-precursor": "#9370db",
    "melanocyte":           "#4b3ca3",
}

# hematopoiesis (15 classes)
_HSC = {
    "LT-HSC":         "#1a3d78",  # stem dark blue
    "MPP":            "#7d5fc9",  # progenitor purple (was teal → indistinguishable from lymphoid/endothelial)
    "erythroid":      "#c1272d",  # red lineage
    "megakaryocyte":  "#a1204b",
    "basophil-mast":  "#e07b39",
    "myeloid":        "#8a5822",  # myeloid browns (dark)
    "monocyte":       "#d4a373",  # tan — distinct from myeloid brown & macrophage
    "macrophage":     "#6b4321",
    "lymphoid":       "#1e7a4f",  # lymph greens (was #2e8b8b → exact duplicate of endothelial)
    "T-cell":         "#3aa17f",
    "naive-B":        "#5cbf88",
    "pro-B":          "#7fd39d",
    "endothelial":    "#2e8b8b",  # shared with skin
    "fibroblast":     "#8f1e1e",
    "stromal":        "#6b4a3b",
}

# pancreas (20 classes)
_PANC = {
    "alpha":                          "#a3123a",  # alpha reds
    "adult-alpha":                    "#7a0e2b",
    "alpha_progenitor":               "#d94360",
    "beta":                           "#1f4e9e",  # beta blues
    "adult-beta":                     "#123469",
    "beta_progenitor":                "#4d78c4",
    "delta":                          "#7d3c98",  # delta purple
    "gamma":                          "#af7ac5",
    "epsilon":                        "#f39c12",  # epsilon orange
    "Fev-EP":                         "#e67e22",  # endocrine progenitor oranges
    "endocrine-progenitor":           "#c68e4b",
    "endocrine-progenitor-primed":    "#a86b28",
    "pancreatic-progenitor":          "#16a085",  # progenitor greens
    "proliferating":                  "#48c9b0",
    "acinar":                         "#8a5822",  # exocrine browns
    "exocrine":                       "#5d3a11",
    "ductal":                         "#7b6b57",
    "endothelial":                    "#2e8b8b",  # shared
    "immune":                         "#d1c02b",
    "mesenchyme":                     "#6b4a3b",
}

# every class from every system, plus a safe fallback
CLASS_COLORS = {**_SKIN, **_HSC, **_PANC}

# canonical genotype / condition colors
GENOTYPE_COLORS = {
    "WT":       "#1f77b4",
    "En1-cKO":  "#d62728",
    "Kit_W41":  "#d62728",
    "control":  "#1f77b4",
    "other":    "#bbbbbb",
}

# stage colors (viridis-ish for ordinal)
STAGE_COLORS = {
    "3": "#440154",
    "4": "#3b528b",
    "5": "#21918c",
    "6": "#fde725",
}


# shared font-size constants (style spec): small titles, larger body text.
SUPTITLE_FS = 15   # figure suptitles
TITLE_FS = 14      # panel / axes titles
LABEL_FS = 13      # axis labels
TICK_FS = 12       # tick labels
LEGEND_FS = 11     # legend text
ANNOT_FS = 11      # in-plot annotations
CBAR_FS = 12       # colorbar labels


def color_for(cls, fallback="#888888"):
    """look up a class name; return fallback if missing."""
    if cls in CLASS_COLORS:
        return CLASS_COLORS[cls]
    # simple aliases
    s = str(cls).strip()
    return CLASS_COLORS.get(s, fallback)


def apply_style():
    """shared rcparams; call at top of every figure script."""
    import matplotlib.pyplot as plt
    plt.rcParams.update({
        "font.family": "DejaVu Sans",
        "font.size": 12,
        "axes.titlesize": TITLE_FS,
        "axes.labelsize": LABEL_FS,
        "xtick.labelsize": TICK_FS,
        "ytick.labelsize": TICK_FS,
        "legend.fontsize": LEGEND_FS,
        "legend.title_fontsize": LEGEND_FS + 1,
        "figure.titlesize": SUPTITLE_FS,
        "pdf.fonttype": 42,
        "ps.fonttype": 42,
        "axes.spines.top": False,
        "axes.spines.right": False,
        "axes.linewidth": 1.2,
        "xtick.major.width": 1.2,
        "ytick.major.width": 1.2,
    })