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Merged
Alek99 merged 1 commit into from
Jul 27, 2026
Merged

Polish real-world example gallery #342

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112 changes: 36 additions & 76 deletions examples/real_world/01_gaia_hr_diagram.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -113,20 +113,19 @@
"metadata": {},
"outputs": [],
"source": [
"axis_style = {\n",
" \"axis_color\": \"#65708d\",\n",
" \"axis_width\": 1.0,\n",
" \"grid_color\": \"#343755\",\n",
" \"grid_dash\": \"dotted\",\n",
" \"grid_opacity\": 0.58,\n",
" \"grid_width\": 0.8,\n",
" \"label_color\": \"#d7d9e8\",\n",
" \"label_size\": 14,\n",
" \"tick_color\": \"#65708d\",\n",
" \"tick_label_color\": \"#aeb4cb\",\n",
" \"tick_label_size\": 12.5,\n",
" \"tick_length\": 5,\n",
" \"tick_width\": 0.8,\n",
"x_axis_style = {\n",
" \"axis_color\": \"#8e51ff80\",\n",
" \"axis_width\": 1.2,\n",
" \"grid_opacity\": 0,\n",
" \"label_color\": \"#00000000\",\n",
" \"tick_color\": \"#00000000\",\n",
" \"tick_label_color\": \"#00000000\",\n",
" \"tick_width\": 0,\n",
"}\n",
"y_axis_style = {\n",
" **x_axis_style,\n",
" \"axis_color\": \"#00000000\",\n",
" \"axis_width\": 0,\n",
"}\n",
"sequence_label_style = {\n",
" \"background\": \"#090b18f2\",\n",
Expand All @@ -137,6 +136,7 @@
" \"letter_spacing\": \"0.055em\",\n",
" \"padding\": \"4px 8px\",\n",
"}\n",
"detail_step = max(1, color_index.size // 40_000)\n",
"\n",
"chart = xy.scatter_chart(\n",
" xy.scatter(\n",
Expand All @@ -149,14 +149,22 @@
" opacity=0.82,\n",
" density=True,\n",
" ),\n",
" xy.scatter(\n",
" color_index[::detail_step],\n",
" absolute_g[::detail_step],\n",
" color=\"#f0abfc\",\n",
" size=0.65,\n",
" opacity=0.14,\n",
" density=False,\n",
" ),\n",
" xy.callout(\n",
" 2.35,\n",
" 0.8,\n",
" \"RED GIANT BRANCH\",\n",
" dx=88,\n",
" dy=-32,\n",
" color=\"#f6a15f\",\n",
" width=1.2,\n",
" width=1.35,\n",
" opacity=0.8,\n",
" style={**sequence_label_style, \"label_color\": \"#ffc48d\"},\n",
" ),\n",
Expand All @@ -167,7 +175,7 @@
" dx=116,\n",
" dy=-22,\n",
" color=\"#bca8ff\",\n",
" width=1.2,\n",
" width=1.35,\n",
" opacity=0.76,\n",
" style={**sequence_label_style, \"label_color\": \"#ddd4ff\"},\n",
" ),\n",
Expand All @@ -178,78 +186,30 @@
" dx=-86,\n",
" dy=34,\n",
" color=\"#8ed8ff\",\n",
" width=1.2,\n",
" width=1.35,\n",
" opacity=0.78,\n",
" anchor=\"end\",\n",
" style={**sequence_label_style, \"label_color\": \"#bde9ff\"},\n",
" ),\n",
" xy.text(\n",
" 0.08,\n",
" 0.965,\n",
" \"GAIA DR3\",\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#bca8ff\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 11.5,\n",
" \"font_weight\": 750,\n",
" \"letter_spacing\": \"0.18em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.text(\n",
" 0.08,\n",
" 0.928,\n",
" \"Hertzsprung\\u2013Russell diagram\",\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#fff5e8\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 25,\n",
" \"font_weight\": 760,\n",
" \"letter_spacing\": \"0.005em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.text(\n",
" 0.08,\n",
" 0.872,\n",
" f\"{color_index.size:,} HIGH-CONFIDENCE STARS · BRIGHTER ↑ · BLUE → RED\",\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#9299b8\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 11.5,\n",
" \"font_weight\": 600,\n",
" \"letter_spacing\": \"0.09em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.x_axis(\n",
" label=\"STELLAR COLOR · BP \\u2212 RP (mag)\",\n",
" label=None,\n",
" domain=(-1.0, 5.0),\n",
" tick_values=[-1, 0, 1, 2, 3, 4, 5],\n",
" tick_labels=[\"\\u22121\", \"0\", \"1\", \"2\", \"3\", \"4\", \"5\"],\n",
" style=axis_style,\n",
" tick_label_strategy=\"none\",\n",
" style=x_axis_style,\n",
" ),\n",
" xy.y_axis(\n",
" label=\"ABSOLUTE G MAGNITUDE\",\n",
" label_offset=-28,\n",
" label=None,\n",
" domain=(-6.0, 16.0),\n",
" reverse=True,\n",
" tick_values=[-6, -2, 2, 6, 10, 14],\n",
" tick_labels=[\"\\u22126\", \"\\u22122\", \"2\", \"6\", \"10\", \"14\"],\n",
" style=axis_style,\n",
" tick_label_strategy=\"none\",\n",
" style=y_axis_style,\n",
" ),\n",
" xy.theme(\n",
" background=\"#03040c\",\n",
" plot_background=\"#080916\",\n",
" background=\"#080b16\",\n",
" plot_background=\"#080b16\",\n",
" text_color=\"#e9eaf2\",\n",
" grid_color=\"#343755\",\n",
" axis_color=\"#65708d\",\n",
" grid_color=\"#00000000\",\n",
" axis_color=\"#8e51ff80\",\n",
" crosshair_color=\"#ffc48d\",\n",
" selection_color=\"#bca8ff\",\n",
" selection_fill=\"#bca8ff26\",\n",
Expand All @@ -259,7 +219,7 @@
" \"axis_title\": {\"font_weight\": 680, \"letter_spacing\": \"0.055em\"},\n",
" \"tick_label\": {\"font_variant_numeric\": \"tabular-nums\"},\n",
" },\n",
" padding=(112, 48, 70, 116),\n",
" padding=(24, 32, 24, 48),\n",
" width=1200,\n",
" height=700,\n",
")\n",
Expand Down
101 changes: 16 additions & 85 deletions examples/real_world/02_gnomad_allele_frequency.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -179,24 +179,18 @@
"rare_variant_share = 100.0 * np.count_nonzero(allele_frequency < 1e-2) / allele_frequency.size\n",
"\n",
"x_axis_style = {\n",
" \"axis_color\": \"#8094a5\",\n",
" \"axis_color\": \"#2b7fff66\",\n",
" \"axis_width\": 1.0,\n",
" \"grid_opacity\": 0,\n",
" \"label_color\": \"#19364b\",\n",
" \"label_size\": 14,\n",
" \"tick_color\": \"#8094a5\",\n",
" \"tick_label_color\": \"#40596a\",\n",
" \"tick_label_size\": 11.5,\n",
" \"tick_length\": 5,\n",
" \"tick_width\": 0.8,\n",
" \"label_color\": \"#00000000\",\n",
" \"tick_color\": \"#00000000\",\n",
" \"tick_label_color\": \"#00000000\",\n",
" \"tick_width\": 0,\n",
"}\n",
"y_axis_style = {\n",
" **x_axis_style,\n",
" \"grid_color\": \"#b9cbd6\",\n",
" \"grid_dash\": \"dotted\",\n",
" \"grid_opacity\": 0.78,\n",
" \"grid_width\": 0.8,\n",
" \"tick_label_size\": 12.5,\n",
" \"axis_color\": \"#00000000\",\n",
" \"axis_width\": 0,\n",
"}\n",
"\n",
"chart = xy.scatter_chart(\n",
Expand All @@ -216,16 +210,6 @@
" opacity=0.72,\n",
" density=True,\n",
" ),\n",
" *[\n",
" xy.vline(\n",
" boundary,\n",
" color=\"#9db2c0\",\n",
" width=0.7,\n",
" opacity=0.5,\n",
" style={\"dash\": \"2,5\"},\n",
" )\n",
" for boundary in chromosome_boundaries\n",
" ],\n",
" xy.hline(\n",
" 1e-2,\n",
" color=\"#087e8b\",\n",
Expand Down Expand Up @@ -260,77 +244,24 @@
" \"letter_spacing\": \"0.075em\",\n",
" },\n",
" ),\n",
" xy.text(\n",
" 0.08,\n",
" 0.965,\n",
" \"gnomAD v4.1 / Allele-frequency atlas\",\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#102f44\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 24,\n",
" \"font_weight\": 760,\n",
" \"letter_spacing\": \"0.01em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.text(\n",
" 0.08,\n",
" 0.912,\n",
" (\n",
" f\"{genomic_position.size:,} VARIANTS · {len(chromosomes)} AUTOSOMES · \"\n",
" f\"{windows_per_chromosome} INDEXED WINDOWS EACH\"\n",
" ),\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#597487\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 11.5,\n",
" \"font_weight\": 600,\n",
" \"letter_spacing\": \"0.085em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.text(\n",
" 0.95,\n",
" 0.955,\n",
" \"AF · LOG₁₀ SCALE\",\n",
" dx=0,\n",
" dy=0,\n",
" color=\"#087e8b\",\n",
" anchor=\"end\",\n",
" style={\n",
" \"coordinate_space\": \"figure_fraction\",\n",
" \"font_size\": 11,\n",
" \"font_weight\": 700,\n",
" \"letter_spacing\": \"0.09em\",\n",
" \"vertical_align\": \"top\",\n",
" },\n",
" ),\n",
" xy.x_axis(\n",
" label=\"CHROMOSOME\",\n",
" tick_values=tick_values,\n",
" tick_labels=tick_labels,\n",
" tick_label_min_gap=0,\n",
" label=None,\n",
" tick_label_strategy=\"none\",\n",
" style=x_axis_style,\n",
" ),\n",
" xy.y_axis(\n",
" label=\"ALTERNATE ALLELE FREQUENCY\",\n",
" label_offset=-28,\n",
" label=None,\n",
" type_=\"log\",\n",
" domain=(1e-7, 1.0),\n",
" tick_values=[1e-7, 1e-6, 1e-5, 1e-4, 1e-3, 1e-2, 1e-1, 1.0],\n",
" tick_labels=[\"10⁻⁷\", \"10⁻⁶\", \"10⁻⁵\", \"10⁻⁴\", \"10⁻³\", \"10⁻²\", \"10⁻¹\", \"1\"],\n",
" tick_label_strategy=\"none\",\n",
" style=y_axis_style,\n",
" ),\n",
" xy.theme(\n",
" background=\"#f2f8fb\",\n",
" plot_background=\"#fbfdfe\",\n",
" background=\"#f8fafc\",\n",
" plot_background=\"#f8fafc\",\n",
" text_color=\"#19364b\",\n",
" grid_color=\"#b9cbd6\",\n",
" axis_color=\"#8094a5\",\n",
" grid_color=\"#00000000\",\n",
" axis_color=\"#2b7fff66\",\n",
" crosshair_color=\"#087e8b\",\n",
" selection_color=\"#075985\",\n",
" selection_fill=\"#0891b226\",\n",
Expand All @@ -340,7 +271,7 @@
" \"axis_title\": {\"font_weight\": 680, \"letter_spacing\": \"0.055em\"},\n",
" \"tick_label\": {\"font_variant_numeric\": \"tabular-nums\"},\n",
" },\n",
" padding=(96, 48, 78, 116),\n",
" padding=(36, 48, 42, 72),\n",
" width=1200,\n",
" height=700,\n",
")\n",
Expand Down
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