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Merged
MarkusNeusinger merged 4 commits into from
May 15, 2026
Merged

feat(highcharts): implement circos-basic #6805

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8abeccc
chore(highcharts): add metadata for circos-basic
github-actions[bot] May 15, 2026
44da74b
chore(highcharts): update quality score 86 and review feedback for ci…
github-actions[bot] May 15, 2026
a7dd9b3
chore(highcharts): update quality score 89 and review feedback for ci…
github-actions[bot] May 15, 2026
4d19398
Merge branch 'main' into implementation/circos-basic/highcharts
MarkusNeusinger May 15, 2026
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223 changes: 113 additions & 110 deletions plots/circos-basic/implementations/python/highcharts.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
""" pyplots.ai
""" anyplot.ai
circos-basic: Circos Plot
Library: highcharts unknown | Python 3.13.11
Quality: 91/100 | Created: 2025-12-31
Library: highcharts unknown | Python 3.13.13
Quality: 89/100 | Updated: 2026-05-15
"""

import json
import os
import tempfile
import time
import urllib.request
Expand All @@ -15,151 +16,149 @@
from selenium.webdriver.chrome.options import Options


# Data - Simulating trade flows between 8 regions
THEME = os.getenv("ANYPLOT_THEME", "light")
PAGE_BG = "#FAF8F1" if THEME == "light" else "#1A1A17"
ELEVATED_BG = "#FFFDF6" if THEME == "light" else "#242420"
INK = "#1A1A17" if THEME == "light" else "#F0EFE8"
INK_SOFT = "#4A4A44" if THEME == "light" else "#B8B7B0"
INK_MUTED = "#6B6A63" if THEME == "light" else "#A8A79F"
GRID = "rgba(26,26,23,0.10)" if THEME == "light" else "rgba(240,239,232,0.10)"

OKABE_ITO = ["#009E73", "#D55E00", "#0072B2", "#CC79A7", "#E69F00", "#56B4E9", "#F0E442"]

# Data - Simulating trade flows between 8 chromosomes with expression tracks
np.random.seed(42)

regions = ["N.America", "S.America", "Europe", "Africa", "MidEast", "S.Asia", "E.Asia", "Oceania"]
chromosomes = ["Chr1", "Chr2", "Chr3", "Chr4", "Chr5", "Chr6", "Chr7", "Chr8"]

# Generate flow matrix - inter-regional trade flows
n_regions = len(regions)
flow_matrix = np.zeros((n_regions, n_regions))
# Generate flow matrix - inter-chromosomal connections (similar to genomic translocations)
n_chrs = len(chromosomes)
flow_matrix = np.zeros((n_chrs, n_chrs))

# Create realistic flow patterns with some regions having stronger connections
for i in range(n_regions):
for j in range(n_regions):
for i in range(n_chrs):
for j in range(n_chrs):
if i != j:
base_flow = np.random.exponential(50)
# Some regional pairs have stronger trade relationships
if (i == 0 and j == 6) or (i == 6 and j == 0): # North America - East Asia
base_flow = np.random.exponential(40)
# Some chr pairs have stronger connections (realistic genomic patterns)
if (i == 0 and j == 6) or (i == 6 and j == 0):
base_flow *= 3
elif (i == 2 and j == 6) or (i == 6 and j == 2): # Europe - East Asia
elif (i == 2 and j == 5) or (i == 5 and j == 2):
base_flow *= 2.5
elif (i == 0 and j == 2) or (i == 2 and j == 0): # North America - Europe
elif (i == 1 and j == 4) or (i == 4 and j == 1):
base_flow *= 2
flow_matrix[i, j] = base_flow

# Prepare data for Highcharts dependency wheel (circular chord-like visualization)
# Format: [from, to, weight] arrays
# Filter connections for clarity
connections = []
for i in range(n_regions):
for j in range(n_regions):
if i != j and flow_matrix[i, j] > 20: # Filter small connections
connections.append([regions[i], regions[j], float(round(flow_matrix[i, j], 1))])

# Colorblind-safe colors for each region
colors = [
"#306998", # Python Blue - N. America
"#FFD43B", # Python Yellow - S. America
"#9467BD", # Purple - Europe
"#17BECF", # Cyan - Africa
"#8C564B", # Brown - Mid. East
"#E377C2", # Pink - S. Asia
"#2CA02C", # Green - E. Asia
"#BCBD22", # Olive - Oceania
]

# Full region names for legend
region_full_names = [
"North America",
"South America",
"Europe",
"Africa",
"Middle East",
"South Asia",
"East Asia",
"Oceania",
]

# Generate inner track data (regional GDP representation as percentage)
gdp_data = [26.0, 4.5, 22.0, 3.5, 5.0, 8.0, 28.0, 3.0] # Approximate world GDP share %
for i in range(n_chrs):
for j in range(n_chrs):
if i != j and flow_matrix[i, j] > 15:
connections.append([chromosomes[i], chromosomes[j], float(round(flow_matrix[i, j], 1))])

# Use Okabe-Ito palette for chromosomes (cycling through palette)
chr_colors = [OKABE_ITO[i % len(OKABE_ITO)] for i in range(n_chrs)]

# Create nodes with colors
nodes = [{"id": regions[i], "color": colors[i]} for i in range(n_regions)]
nodes = [{"id": chromosomes[i], "color": chr_colors[i]} for i in range(n_chrs)]

# Create inner track data (expression values as percentages)
expression_data = [28.0, 19.0, 16.0, 13.0, 10.0, 7.0, 5.0, 2.0]

# Create inner track pie chart data (GDP representation)
inner_track_data = [{"name": region_full_names[i], "y": gdp_data[i], "color": colors[i]} for i in range(n_regions)]
inner_track_data = [{"name": chromosomes[i], "y": expression_data[i], "color": chr_colors[i]} for i in range(n_chrs)]

# Create Highcharts configuration directly
# Create Highcharts configuration with theme-adaptive colors
chart_config = {
"chart": {
"type": "dependencywheel",
"width": 3600,
"height": 3600,
"backgroundColor": "#ffffff",
"marginRight": 420,
"backgroundColor": PAGE_BG,
"marginRight": 500,
"style": {"color": INK},
},
"title": {
"text": "circos-basic · highcharts · anyplot.ai",
"style": {"fontSize": "52px", "fontWeight": "bold", "color": INK},
},
"subtitle": {
"text": "Chromosomal Connections with Expression Tracks",
"style": {"fontSize": "32px", "color": INK_SOFT},
},
"title": {"text": "circos-basic · highcharts · pyplots.ai", "style": {"fontSize": "52px", "fontWeight": "bold"}},
"subtitle": {"text": "Global Trade Flows Between Regions (with GDP Inner Track)", "style": {"fontSize": "36px"}},
"accessibility": {"enabled": False},
"credits": {"enabled": False},
"tooltip": {"style": {"fontSize": "28px"}},
"tooltip": {"style": {"fontSize": "20px", "color": INK}},
"legend": {
"enabled": True,
"align": "right",
"verticalAlign": "middle",
"layout": "vertical",
"itemStyle": {"fontSize": "32px", "fontWeight": "normal"},
"symbolHeight": 28,
"symbolWidth": 28,
"symbolRadius": 14,
"itemMarginTop": 18,
"itemMarginBottom": 18,
"x": -30,
"title": {"text": "Regions", "style": {"fontSize": "36px", "fontWeight": "bold"}},
"itemStyle": {"fontSize": "24px", "color": INK_SOFT},
"backgroundColor": ELEVATED_BG,
"borderColor": INK_SOFT,
"borderWidth": 2,
"symbolHeight": 24,
"symbolWidth": 24,
"symbolRadius": 12,
"itemMarginTop": 16,
"itemMarginBottom": 16,
"x": -50,
"title": {"text": "Chromosomes", "style": {"fontSize": "28px", "fontWeight": "bold", "color": INK}},
},
"plotOptions": {"dependencywheel": {"showInLegend": False}, "pie": {"showInLegend": False}},
"colors": OKABE_ITO,
"series": [
{
"type": "dependencywheel",
"name": "Trade Flow",
"name": "Connections",
"keys": ["from", "to", "weight"],
"data": connections,
"nodes": nodes,
"size": "78%",
"center": ["42%", "50%"],
"size": "72%",
"center": ["35%", "50%"],
"dataLabels": {
"enabled": True,
"style": {"fontSize": "40px", "fontWeight": "bold", "textOutline": "5px white"},
"distance": 50,
"style": {"fontSize": "28px", "fontWeight": "bold", "color": INK, "textOutline": f"3px {PAGE_BG}"},
"distance": 30,
"rotationMode": "circular",
"padding": 8,
"padding": 6,
},
"nodeWidth": 45,
"nodeWidth": 50,
"nodeColor": "#ffffff",
},
{
"type": "pie",
"name": "GDP Share",
"name": "Expression",
"data": inner_track_data,
"size": "28%",
"innerSize": "20%",
"center": ["42%", "50%"],
"size": "32%",
"innerSize": "24%",
"center": ["35%", "50%"],
"showInLegend": False,
"dataLabels": {
"enabled": True,
"format": "{point.percentage:.0f}%",
"distance": -25,
"style": {"fontSize": "22px", "fontWeight": "bold", "color": "#ffffff", "textOutline": "2px #333333"},
"distance": -20,
"style": {"fontSize": "24px", "fontWeight": "bold", "color": INK, "textOutline": f"2px {PAGE_BG}"},
},
"tooltip": {"pointFormat": "<b>{point.name}</b>: {point.y}% of World GDP"},
"tooltip": {"pointFormat": "<b>{point.name}</b>: {point.y:.1f}%"},
},
]
+ [
{
"type": "pie",
"name": region_full_names[i],
"data": [{"name": region_full_names[i], "y": 1, "color": colors[i]}],
"name": chromosomes[i],
"data": [{"name": chromosomes[i], "y": 1, "color": chr_colors[i]}],
"size": 0,
"showInLegend": True,
"dataLabels": {"enabled": False},
}
for i in range(n_regions)
for i in range(n_chrs)
],
}

# Download Highcharts JS and sankey module (dependency wheel requires sankey)
highcharts_url = "https://code.highcharts.com/highcharts.js"
sankey_url = "https://code.highcharts.com/modules/sankey.js"
dependency_wheel_url = "https://code.highcharts.com/modules/dependency-wheel.js"
# Download Highcharts JS modules from CDN
highcharts_url = "https://cdnjs.cloudflare.com/ajax/libs/highcharts/11.4.8/highcharts.js"
sankey_url = "https://cdnjs.cloudflare.com/ajax/libs/highcharts/11.4.8/modules/sankey.min.js"
dependency_wheel_url = "https://cdnjs.cloudflare.com/ajax/libs/highcharts/11.4.8/modules/dependency-wheel.min.js"

with urllib.request.urlopen(highcharts_url, timeout=30) as response:
highcharts_js = response.read().decode("utf-8")
Expand All @@ -170,7 +169,7 @@
with urllib.request.urlopen(dependency_wheel_url, timeout=30) as response:
dependency_wheel_js = response.read().decode("utf-8")

# Generate HTML with inline scripts
# Generate HTML with inline scripts for PNG export
chart_config_json = json.dumps(chart_config)
html_content = f"""<!DOCTYPE html>
<html>
Expand All @@ -180,51 +179,55 @@
<script>{sankey_js}</script>
<script>{dependency_wheel_js}</script>
</head>
<body style="margin:0; background-color: #ffffff;">
<body style="margin:0; background-color: {PAGE_BG};">
<div id="container" style="width: 3600px; height: 3600px;"></div>
<script>
Highcharts.chart('container', {chart_config_json});
</script>
</body>
</html>"""

# Write temp HTML and take screenshot
# Write temp HTML and take screenshot for PNG
with tempfile.NamedTemporaryFile(mode="w", suffix=".html", delete=False, encoding="utf-8") as f:
f.write(html_content)
temp_path = f.name

# Also save HTML for interactive version
# Setup Chrome for screenshot
chrome_options = Options()
chrome_options.add_argument("--headless")
chrome_options.add_argument("--no-sandbox")
chrome_options.add_argument("--disable-dev-shm-usage")
chrome_options.add_argument("--disable-gpu")
chrome_options.add_argument("--hide-scrollbars")
chrome_options.add_argument("--window-size=3600,3600")

driver = webdriver.Chrome(options=chrome_options)
driver.execute_cdp_cmd(
"Emulation.setDeviceMetricsOverride", {"width": 3600, "height": 3600, "deviceScaleFactor": 1, "mobile": False}
)
driver.get(f"file://{temp_path}")
time.sleep(5)
driver.save_screenshot(f"plot-{THEME}.png")
driver.quit()

Path(temp_path).unlink()

# Generate HTML with CDN links for interactive version
interactive_html = f"""<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<title>circos-basic · highcharts · pyplots.ai</title>
<title>circos-basic · highcharts · anyplot.ai</title>
<script src="https://code.highcharts.com/highcharts.js"></script>
<script src="https://code.highcharts.com/modules/sankey.js"></script>
<script src="https://code.highcharts.com/modules/dependency-wheel.js"></script>
</head>
<body style="margin:0; background-color: #ffffff;">
<body style="margin:0; background-color: {PAGE_BG};">
<div id="container" style="width: 100%; height: 100vh;"></div>
<script>
Highcharts.chart('container', {chart_config_json});
</script>
</body>
</html>"""
with open("plot.html", "w", encoding="utf-8") as f:
with open(f"plot-{THEME}.html", "w", encoding="utf-8") as f:
f.write(interactive_html)

# Setup Chrome for screenshot
chrome_options = Options()
chrome_options.add_argument("--headless")
chrome_options.add_argument("--no-sandbox")
chrome_options.add_argument("--disable-dev-shm-usage")
chrome_options.add_argument("--disable-gpu")
chrome_options.add_argument("--window-size=3600,3600")

driver = webdriver.Chrome(options=chrome_options)
driver.get(f"file://{temp_path}")
time.sleep(5) # Wait for chart to render
driver.save_screenshot("plot.png")
driver.quit()

Path(temp_path).unlink() # Clean up temp file
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