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14ba315 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 | """Shared Plotly chart configuration and color constants for the Pangenome Atlas.
Every chart-building callback should import from this module to ensure
visual consistency across all plots.
Exports
-------
COLORS – dict of semantic color tokens.
COUNTRY_COLORS – per-country color mapping (17 countries + Unknown).
CLUSTER_COLORS – ordered list for the 3 optimal clusters.
PLOTLY_TEMPLATE – light-background Plotly layout dict.
PLOTLY_TEMPLATE_DARK – dark-background variant for globe / 3-D views.
apply_template() – apply the atlas template to any ``plotly.graph_objects.Figure``.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
if TYPE_CHECKING:
import plotly.graph_objects as go # pragma: no cover
# =====================================================================
# Color Palette
# =====================================================================
COLORS: dict[str, str] = {
# Gene classification
"core": "#2E7D32", # forest green
"shell": "#F9A825", # warm amber
"cloud": "#C62828", # warm red
# UI accents
"selected": "#D4A017", # gold — user's selected line
"accent": "#1565C0", # deep blue — links / actions
# Backgrounds
"bg_dark": "#1a2332", # dark navy — globe / hero header
"bg_light": "#FAFAF5", # warm white — page background
"bg_card": "#FFFFFF", # card surface
# Text
"text_primary": "#1A1A1A",
"text_secondary": "#757575",
"text_muted": "#94a3b8",
# Structural
"border": "#E0E0E0",
"grid_faint": "#F0F0E8",
}
# Per-country colors used by the globe, UMAP, and any country legend.
# 17 countries + Unknown.
COUNTRY_COLORS: dict[str, str] = {
"India": "#2E7D32",
"Philippines": "#1565C0",
"Kenya": "#C62828",
"Nepal": "#D4A017",
"Myanmar": "#6A1B9A",
"Uganda": "#00838F",
"Zaire": "#E65100",
"Indonesia": "#455A64",
"Jamaica": "#AD1457",
"South_Africa": "#1B5E20",
"Puerto_Rico": "#0277BD",
"Sierra_Leone": "#BF360C",
"Nigeria": "#827717",
"Malawi": "#4E342E",
"Italy": "#283593",
"Sri_Lanka": "#00695C",
"Thailand": "#FF6F00",
"Unknown": "#9E9E9E",
}
# Cluster colors for the 3 optimal clusters (silhouette = 0.649).
CLUSTER_COLORS: list[str] = ["#2E7D32", "#1565C0", "#C62828"]
# =====================================================================
# Shared font stack (matches the Gradio theme)
# =====================================================================
_FONT_STACK = "-apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif"
# =====================================================================
# Plotly Layout Templates
# =====================================================================
PLOTLY_TEMPLATE: dict = dict(
layout=dict(
paper_bgcolor="rgba(0,0,0,0)",
plot_bgcolor="rgba(0,0,0,0)",
font=dict(
family=_FONT_STACK,
color=COLORS["text_primary"],
size=13,
),
title=dict(
font=dict(size=18, color=COLORS["text_primary"]),
x=0.02,
xanchor="left",
),
xaxis=dict(
showgrid=False,
zeroline=False,
showline=False,
),
yaxis=dict(
showgrid=False,
zeroline=False,
showline=False,
),
margin=dict(l=30, r=20, t=50, b=30),
hoverlabel=dict(
bgcolor="white",
font_size=13,
font_family=_FONT_STACK,
bordercolor=COLORS["border"],
),
legend=dict(
bgcolor="rgba(255,255,255,0.85)",
bordercolor="rgba(0,0,0,0)",
font=dict(size=12),
),
)
)
# Dark variant for 3-D plots, globe visualisations, and hero panels.
PLOTLY_TEMPLATE_DARK: dict = dict(
layout=dict(
paper_bgcolor=COLORS["bg_dark"],
plot_bgcolor=COLORS["bg_dark"],
font=dict(
family=_FONT_STACK,
color="#E0E0E0",
size=13,
),
title=dict(
font=dict(size=18, color="#E0E0E0"),
x=0.02,
xanchor="left",
),
xaxis=dict(
showgrid=False,
zeroline=False,
showline=False,
color="#E0E0E0",
),
yaxis=dict(
showgrid=False,
zeroline=False,
showline=False,
color="#E0E0E0",
),
margin=dict(l=30, r=20, t=50, b=30),
hoverlabel=dict(
bgcolor="#263245",
font_size=13,
font_family=_FONT_STACK,
bordercolor="#3a4a60",
),
legend=dict(
bgcolor="rgba(26,35,50,0.85)",
bordercolor="rgba(0,0,0,0)",
font=dict(size=12, color="#E0E0E0"),
),
)
)
# Modebar buttons to hide for a cleaner look.
_MODEBAR_REMOVE = [
"toImage",
"zoom2d",
"pan2d",
"select2d",
"lasso2d",
"autoScale2d",
"resetScale2d",
"zoomIn2d",
"zoomOut2d",
]
def apply_template(fig: "go.Figure", dark: bool = False) -> "go.Figure":
"""Apply the Atlas Plotly template to *fig* and hide the modebar.
Parameters
----------
fig : plotly.graph_objects.Figure
The figure to style in-place.
dark : bool, optional
If ``True``, use the dark-background variant suitable for globe
and 3-D scenes. Defaults to ``False``.
Returns
-------
plotly.graph_objects.Figure
The same figure, for chaining.
"""
template = PLOTLY_TEMPLATE_DARK if dark else PLOTLY_TEMPLATE
fig.update_layout(**template["layout"])
fig.update_layout(modebar=dict(remove=_MODEBAR_REMOVE))
return fig
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