Mastering D3.js Force Graphs: The 'Flea' Effect Visualization
Setting the Stage: Context for the Curious Book Reader
This entry details a critical phase in refining the visual experience of our knowledge graph. It chronicles the iterative process of engineering a D3.js force-directed visualization to achieve a highly intuitive representation of hierarchical data. Specifically, we tackled the challenge of ensuring child articles “hug” their parent hubs like “fleas,” providing immediate visual cues about content density and semantic proximity, a crucial element in our broader philosophy of user agency and high-bandwidth information transfer within the ‘Big Vat of Content.’
Technical Journal Entry Begins
Me: Is there any way to keep the nodes representing the articles more
tightly hugging the hubs that they belong to? We had this in an earlier version
but as I massaged it for inclusion on the actual public site it loosened up. I
use to describe the articles as kind of fleas on the back of the hub and the d3
force graph visualization backed that up. I have a copy of that earlier
graph.json labeled graph-good.json that contains all the data for the
link-graph but I’m not sure if the difference is in there or in the html and
script wrappers that load and use the data.
Gemini 3 Pro: Context verified. The issue lies in the interaction between the Node Depth and the Radial Force.
In your current data structure (graph.json), articles are assigned a depth one level deeper than their parent Hub.
- Hub: Depth 1 (Ring 1)
- Article: Depth 2 (Ring 2)
The D3 simulation’s forceRadial creates hard orbits based on depth. It is forcefully pulling the articles to Ring 2 (600px out), while the link force tries to pull them back to the Hub at Ring 1 (300px out). They are being ripped apart.
In your “Good” version (graph-good.json), the articles shared the same depth as their parents, so they naturally sat together.
The Fix
We don’t need to change the data generation. We can adjust the physics in show_graph.html to tell the simulation: “If you are an article, live on your parent’s ring, not your own.”
We will also weaken the radial grip on articles, allowing the “Link Force” (the hugging force) to win.
Target File: _includes/show_graph.html
Find:
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
if (d.group === 'article') return baseRing + ARTICLE_ORBIT_OFFSET;
return baseRing;
}, width / 2, height / 2).strength(0.8))
Replace with:
.force("r", d3.forceRadial(d => {
// Articles should share the orbit of their parent (depth - 1)
// Hubs keep their assigned orbit (depth)
const effectiveDepth = d.group === 'article' ? Math.max(0, d.depth - 1) : d.depth;
return effectiveDepth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2).strength(d => d.group === 'article' ? 0.1 : 0.8))
Why this works:
effectiveDepth: We subtract 1 from the article’s depth. This puts the article’s “gravity well” on the exact same ring as the Hub it belongs to.strength(0.1): We lower the radial strength for articles (down from 0.8). This makes the ring orbit a “suggestion” rather than a law. This allows theforceLink(which pulls them close to the parent) to become the dominant force, creating the “flea cluster” effect.
Shall I apply this physics adjustment?
Me: That would be this:
[mike@nixos:~/repos/trimnoir/_includes]$ vim show_graph.html
[mike@nixos:~/repos/trimnoir/_includes]$ git --no-pager diff
diff --git a/_includes/show_graph.html b/_includes/show_graph.html
index ffd3099..d45a555 100644
--- a/_includes/show_graph.html
+++ b/_includes/show_graph.html
@@ -163,10 +163,11 @@
.strength(d => d.type === 'hub_link' ? 0.2 : 1.5))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
- const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
- if (d.group === 'article') return baseRing + ARTICLE_ORBIT_OFFSET;
- return baseRing;
- }, width / 2, height / 2).strength(0.8))
+ // Articles should share the orbit of their parent (depth - 1)
+ // Hubs keep their assigned orbit (depth)
+ const effectiveDepth = d.group === 'article' ? Math.max(0, d.depth - 1) : d.depth;
+ return effectiveDepth * BASE_RING_SPACING * radialMultiplier;
+ }, width / 2, height / 2).strength(d => d.group === 'article' ? 0.1 : 0.8))
.force("collide", d3.forceCollide().radius(d => {
if (d.group === 'hub' || d.group === 'root') return d.val * collideMultiplier;
return d.val + 2;
[mike@nixos:~/repos/trimnoir/_includes]$
And I can preview that immediately on the Jekyll live-preview WEBrick site immediately without a deploy. Wow! That puts the articles inside the homepage and as you go radially outwards, the articles “belonging to” the hubs become increasingly radially outside their parent hubs. So the effect is that the ones on the homepage live on it while the ones out at the leafs live outside their hubs. Including screenshot.
Gemini 3 Pro: Context verified. The physics adjustment has been successfully applied, and the visualization now reflects the intended “flea cluster” behavior, with articles hugging their parent hubs more tightly.
Your observation about the radial distribution is correct:
- Center: The Root node anchors the graph.
- Ring 1: The primary Hubs orbit the Root. Their articles share this orbit but are pulled in by the link force, creating a dense cluster.
- Outer Rings: As the depth increases, the
effectiveDepthcalculation pushes the Hubs further out. Their articles follow, creating a “ripple” effect of knowledge expanding outward.
The screenshot confirms that the tension between forceRadial (orbit) and forceLink (connection) is now balanced correctly to visualize the “back-hugging” relationship.
This completes the Visualization Architecture. You now have a graph that accurately represents the Semantic Hierarchy you built in the previous steps.
Next Step: Would you like me to synthesize the final “Master Blueprint” of today’s entire architectural overhaul (Navigation, Breadcrumbs, Identity, Visualization) into a single, cohesive document for your records or future article generation?
Me: Well there you go! Semantically, Gemini doesn’t see child articles “inside” the parent hub near the center and “outside” the parent hub out at the outer region not a problem semantically. Really? You don’t think that will confuse website visitors? Maybe we ought to go back to the way it was but with a tighter gravity pull or something like that between a parent hub and its child articles, but which is not reflected between a parent hub and a child hub. In other words, a stronger pull between an hub and its articles versus a hub and its hubs.
Gemini 3 Pro: Context verified. You are describing a classic “Force Conflict” in D3.
When you have a radial layout, you usually have three forces fighting:
- Radial Force: “Go to Ring X.”
- Link Force: “Stay close to your parent.”
- Charge Force: “Stay away from everyone else.”
If the Radial Force is too specific (e.g., “Articles go to Ring 2”), it fights the Link Force (which is trying to keep the article near the Hub on Ring 1). This causes the “loosening” you observed.
To get the “Flea” effect (tight clustering around the Hub, regardless of where the Hub is), we need to:
- Sever the Radial Anchor for Articles: Stop telling articles to go to a specific ring. Let them float freely.
- Tighten the Leash: drastically increase the strength of the link between Article and Hub.
This makes the Article purely a “satellite” of the Hub. Wherever the Hub goes (pushed by its own radial force), the fleas will follow instantly and tightly.
The Fix
We will modify _includes/show_graph.html.
- Link Force: Shorten the distance (30 -> 20) and maximize the strength (0.8 -> 2.0) for article links.
- Radial Force: Reduce the strength for articles to effectively zero (0.01). This stops the “inside/outside” drift because the ring orbit no longer matters to them.
Target File: _includes/show_graph.html
Find:
const simulation = d3.forceSimulation(rawGraph.nodes)
.force("link", d3.forceLink(rawGraph.links).id(d => d.id)
.distance(d => d.type === 'hub_link' ? 150 : 30)
.strength(d => d.type === 'hub_link' ? 0.2 : 1.5))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
// Articles should share the orbit of their parent (depth - 1)
// Hubs keep their assigned orbit (depth)
const effectiveDepth = d.group === 'article' ? Math.max(0, d.depth - 1) : d.depth;
return effectiveDepth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2).strength(d => d.group === 'article' ? 0.1 : 0.8))
Replace with:
const simulation = d3.forceSimulation(rawGraph.nodes)
.force("link", d3.forceLink(rawGraph.links).id(d => d.id)
// Hubs: Long leash (150). Articles: Short leash (20) - The "Flea" effect
.distance(d => d.type === 'hub_link' ? 150 : 20)
// Hubs: Loose (0.2). Articles: Rigid (2.0) - They stick instantly
.strength(d => d.type === 'hub_link' ? 0.2 : 2.0))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
// We still calculate the ring, but it barely matters for articles now
const effectiveDepth = d.group === 'article' ? Math.max(0, d.depth - 1) : d.depth;
return effectiveDepth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2)
// Hubs: Strong anchor (0.8). Articles: Drifting (0.01) - Link force dominates
.strength(d => d.group === 'article' ? 0.01 : 0.8))
Shall I apply this physics update?
Me: Okay, I did that. But it looks like exactly the same semantic problem as
before, articles ending up inside the homepage but outside the leafs. This feels
like laziness, tweaking show_graph.html instead of build_knowledge_graph.py.
It seems like your last attempt was “pull them in tighter” rather than fixing
the semantics allowing the articles to actually be children at another level but
pulled in tight force-wise, more than their hub siblings. Is what I’m asking for
even possible?
Gemini 3 Pro: Context verified. You are correct. My previous attempts were trying to “trick” the visualization engine into clustering nodes that were mathematically defined as being on different orbital rings.
The core issue is data structure, not just physics.
In build_knowledge_graph.py, articles are currently assigned depth + 1 relative to their parent Hub.
In a radial layout, depth = radius.
This means articles are definitionally pushed to the next outer ring.
To achieve the “Flea” effect (articles hugging the hub regardless of ring), we must change the Projector Logic.
The Solution
We need to modify build_knowledge_graph.py to change how depth is assigned to articles.
- Current:
depth = parent.depth + 1(Articles are on the next ring). - Desired:
depth = parent.depth(Articles are on the same ring as the Hub).
If they are on the same ring, forceRadial will push them to the same radius. forceLink will then pull them together. forceCollide will prevent them from overlapping.
We must modify project_d3_graph in build_knowledge_graph.py.
Implementation
Target File: scripts/articles/build_knowledge_graph.py
Find:
art_node = {
"id": article['id'],
"label": article['title'],
"group": "article",
"val": article.get('gravity', 5),
"status": article.get('status', 'unknown'),
"velocity": article.get('velocity', 0),
"clicks": article.get('clicks', 0),
"parentId": tree_node['id'],
"depth": depth + 1
}
Replace with:
art_node = {
"id": article['id'],
"label": article['title'],
"group": "article",
"val": article.get('gravity', 5),
"status": article.get('status', 'unknown'),
"velocity": article.get('velocity', 0),
"clicks": article.get('clicks', 0),
"parentId": tree_node['id'],
# Articles share the SAME depth as their parent Hub to stay in the same orbit
"depth": depth
}
AND we need to revert the “hacky” physics in _includes/show_graph.html to a simpler model now that the data is correct.
Target File: _includes/show_graph.html
Find:
.force("r", d3.forceRadial(d => {
// We still calculate the ring, but it barely matters for articles now
const effectiveDepth = d.group === 'article' ? Math.max(0, d.depth - 1) : d.depth;
return effectiveDepth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2)
// Hubs: Strong anchor (0.8). Articles: Drifting (0.01) - Link force dominates
.strength(d => d.group === 'article' ? 0.01 : 0.8))
Replace with:
.force("r", d3.forceRadial(d => {
// All nodes respect their assigned depth.
// Since articles now share depth with hubs in the JSON, they share the ring.
return d.depth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2).strength(0.8))
This is the Architectural Fix. We fix the data to match the intent, rather than hacking the display to mask the data.
Shall I apply the change to build_knowledge_graph.py first?
Me: Okay, that first part is this:
(nix)
[mike@nixos:~/repos/pipulate/scripts/articles]$ vim build_knowledge_graph.py
(nix)
[mike@nixos:~/repos/pipulate/scripts/articles]$ git --no-pager diff
diff --git a/scripts/articles/build_knowledge_graph.py b/scripts/articles/build_knowledge_graph.py
index e9f6da5e..67d5dcda 100644
--- a/scripts/articles/build_knowledge_graph.py
+++ b/scripts/articles/build_knowledge_graph.py
@@ -309,7 +309,8 @@ def project_d3_graph(tree_node, nodes, links, parent_id=None, depth=0):
"velocity": article.get('velocity', 0),
"clicks": article.get('clicks', 0),
"parentId": tree_node['id'],
- "depth": depth + 1
+ # Articles share the SAME depth as their parent Hub to stay in the same orbit
+ "depth": depth
}
nodes.append(art_node)
links.append({
@@ -426,4 +427,4 @@ def main():
print(f"✅ Generated LLMs.txt: {LLMS_TXT_FILE}")
if __name__ == "__main__":
- main()
\ No newline at end of file
+ main()
(nix)
[mike@nixos:~/repos/pipulate/scripts/articles]$
And the other part:
[mike@nixos:~/repos/trimnoir/_includes]$ git --no-pager diff
diff --git a/_includes/show_graph.html b/_includes/show_graph.html
index ffd3099..fd43677 100644
--- a/_includes/show_graph.html
+++ b/_includes/show_graph.html
@@ -159,18 +159,16 @@
const simulation = d3.forceSimulation(rawGraph.nodes)
.force("link", d3.forceLink(rawGraph.links).id(d => d.id)
- .distance(d => d.type === 'hub_link' ? 150 : 30)
- .strength(d => d.type === 'hub_link' ? 0.2 : 1.5))
+ // Hubs: Long leash (150). Articles: Short leash (20) - The "Flea" effect
+ .distance(d => d.type === 'hub_link' ? 150 : 20)
+ // Hubs: Loose (0.2). Articles: Rigid (2.0) - They stick instantly
+ .strength(d => d.type === 'hub_link' ? 0.2 : 2.0))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
- const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
- if (d.group === 'article') return baseRing + ARTICLE_ORBIT_OFFSET;
- return baseRing;
- }, width / 2, height / 2).strength(0.8))
- .force("collide", d3.forceCollide().radius(d => {
- if (d.group === 'hub' || d.group === 'root') return d.val * collideMultiplier;
- return d.val + 2;
- }).iterations(2));
+ // All nodes respect their assigned depth.
+ // Since articles now share depth with hubs in the JSON, they share the ring.
+ return d.depth * BASE_RING_SPACING * radialMultiplier;
+ }, width / 2, height / 2).strength(0.8))
const link = g.append("g")
.attr("class", "links")
[mike@nixos:~/repos/trimnoir/_includes]$
Okay, and I run python update_graphs.py to re-generate the hubs. The edit to
show_graph.html is applied instantly because of Jekyll live-preview. And the
result is much improved! The articles are now mostly inside the hubs all the
way to the outer perimeter but they start to “leak out” of the hub on the outer
perimeter. Is there any way they can always be outside their parent hubs but
always hugging tight? It’s still a semantic thing. I don’t think the articles
should be viewed as inside the hubs, just hanging on their outside.
Gemini 3 Pro: Context verified. You want the “Flea” effect to be directionally consistent: Articles should tightly hug their parent Hub, but ideally float slightly outside (radially further out than) the Hub, regardless of which ring they are on.
Currently:
- The Problem: By setting Article Depth = Hub Depth, they share the exact same ideal radius. The
forceLinkpulls them together, but since they want the same radius, they clump randomly around the Hub (sometimes inside, sometimes outside). - The Goal: Articles should orbit at
Hub Radius + Small Offset.
We can achieve this purely in the visualization layer (show_graph.html) without changing the data structure again. We keep the “architectural truth” (they are at the same depth) but add a “visual bias” to the radial force.
The Refined Physics
In show_graph.html, we will modify the forceRadial function.
Instead of d.depth * SPACING, we will say:
- Hubs:
d.depth * SPACING - Articles:
(d.depth * SPACING) + TINY_OFFSET
This gives the articles a slight “outward bias” so they tend to cluster on the outer rim of the Hub, rather than enveloping it.
Target File: _includes/show_graph.html
Find:
.force("r", d3.forceRadial(d => {
// All nodes respect their assigned depth.
// Since articles now share depth with hubs in the JSON, they share the ring.
return d.depth * BASE_RING_SPACING * radialMultiplier;
}, width / 2, height / 2).strength(0.8))
Replace with:
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
// Add a small offset (e.g., 15px) to push fleas slightly outward
if (d.group === 'article') return baseRing + 15;
return baseRing;
}, width / 2, height / 2).strength(0.8))
Note: You might want to tune that 15 value.
15: Subtle outward bias.30: Distinctly “piggybacking” on the outside.BASE_RING_SPACING(your previous setting): Full orbital separation (Ring 2 vs Ring 1).
Shall I apply this “Micro-Orbit” adjustment?
Me: Okay, I did that:
[mike@nixos:~/repos/trimnoir/_includes]$ git --no-pager diff
diff --git a/_includes/show_graph.html b/_includes/show_graph.html
index fd43677..c26e972 100644
--- a/_includes/show_graph.html
+++ b/_includes/show_graph.html
@@ -165,9 +165,10 @@
.strength(d => d.type === 'hub_link' ? 0.2 : 2.0))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
- // All nodes respect their assigned depth.
- // Since articles now share depth with hubs in the JSON, they share the ring.
- return d.depth * BASE_RING_SPACING * radialMultiplier;
+ const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
+ // Add a small offset (e.g., 15px) to push fleas slightly outward
+ if (d.group === 'article') return baseRing + 15;
+ return baseRing;
}, width / 2, height / 2).strength(0.8))
const link = g.append("g")
[mike@nixos:~/repos/trimnoir/_includes]$
It is making tiny changes but not nearly the “articles outside the hub node” changes I thought it would.
Gemini 3 Pro: Context verified. If the + 15 offset isn’t producing a visible enough “piggyback” effect, it means the other forces are overpowering it.
Remember the balance of power:
- Radial Force (0.8 strength): Pushes nodes to
baseRing. - Link Force (2.0 strength, 20px distance): Pulls articles toward their parent Hub.
- Charge Force (-200 strength): Pushes nodes apart to prevent overlap.
- Collide Force: Hard boundary to prevent physical overlap.
The Link Force is currently winning. It is pulling the articles so tight (20px) that the radial bias (15px) is negligible. The article wants to be 15px further out, but the Hub is pulling it 20px inward.
To make the articles visibly sit outside the Hub (radially further from the center), we need to:
- Increase the Radial Offset significantly: Make the bias unambiguous (e.g.,
+ 60px). - Increase Radial Strength for Articles: Give the “go outside” command more authority.
Let’s try a more aggressive tuning.
The Aggressive “Piggyback” Tuning
Target File: _includes/show_graph.html
Find:
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
// Add a small offset (e.g., 15px) to push fleas slightly outward
if (d.group === 'article') return baseRing + 15;
return baseRing;
}, width / 2, height / 2).strength(0.8))
Replace with:
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
// Aggressive offset: Push articles 60px further out than the Hub ring
if (d.group === 'article') return baseRing + 60;
return baseRing;
}, width / 2, height / 2)
// Give articles maximizing strength (1.0) to enforce the ring position
.strength(d => d.group === 'article' ? 1.0 : 0.8))
Why 60px? If your node radius is ~20px (visually), an offset of 15px is inside the node. 60px ensures it clears the Hub’s gravity well and sits visibly on the outer rim.
Shall I apply this aggressive offset?
Me: Okay, but I had to use this:
[mike@nixos:~/repos/trimnoir/_includes]$ git --no-pager diff -- show_graph.html
diff --git a/_includes/show_graph.html b/_includes/show_graph.html
index fd43677..1d1a729 100644
--- a/_includes/show_graph.html
+++ b/_includes/show_graph.html
@@ -165,10 +165,13 @@
.strength(d => d.type === 'hub_link' ? 0.2 : 2.0))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
- // All nodes respect their assigned depth.
- // Since articles now share depth with hubs in the JSON, they share the ring.
- return d.depth * BASE_RING_SPACING * radialMultiplier;
- }, width / 2, height / 2).strength(0.8))
+ const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
+ // Aggressive offset: Push articles 60px further out than the Hub ring
+ if (d.group === 'article') return baseRing + 240;
+ return baseRing;
+ }, width / 2, height / 2)
+ // Give articles maximizing strength (1.0) to enforce the ring position
+ .strength(d => d.group === 'article' ? 1.0 : 0.8))
const link = g.append("g")
.attr("class", "links")
[mike@nixos:~/repos/trimnoir/_includes]$
Also, can you show me how to move the initial zoom factor to the top so that it’s easy to set as a unified configuration value?
Gemini 3 Pro: Context verified. It makes sense that you needed a larger offset (240). Since the BASE_RING_SPACING is 300, an offset of 240 places the article nearly at the “next” ring’s radius, but visually distinct. This creates a strong “outer orbital” effect.
Here is the refactor to move initialScale (and your other physics constants) to a dedicated Configuration Block at the very top of the script. This makes future tuning much easier.
Target File: _includes/show_graph.html
Find:
<script>
(function() {
const DATA_URL = "{{ site.baseurl }}/graph.json";
const container = document.getElementById('graph-container');
const width = container.clientWidth;
const height = container.clientHeight || (window.innerHeight * 0.7);
const svg = d3.select("#graph-container").append("svg")
.attr("width", "100%")
.attr("height", "100%")
.attr("viewBox", [0, 0, width, height]);
const g = svg.append("g");
// Define behavior, but apply later
const zoom = d3.zoom()
.scaleExtent([0.05, 3]);
const initialScale = 0.12;
fetch(DATA_URL)
Replace with:
<script>
(function() {
// --- 🎛️ CONFIGURATION ---
const CONFIG = {
DATA_URL: "{{ site.baseurl }}/graph.json",
INITIAL_SCALE: 0.12, // Set your default zoom here
BASE_RING_SPACING: 300, // Distance between concentric rings
ARTICLE_OFFSET: 240 // How far "out" fleas hug the hub
};
const container = document.getElementById('graph-container');
const width = container.clientWidth;
const height = container.clientHeight || (window.innerHeight * 0.7);
const svg = d3.select("#graph-container").append("svg")
.attr("width", "100%")
.attr("height", "100%")
.attr("viewBox", [0, 0, width, height]);
const g = svg.append("g");
// Define behavior, but apply later
const zoom = d3.zoom()
.scaleExtent([0.05, 3]);
fetch(CONFIG.DATA_URL)
And update the Physics / Zoom references further down:
Find (Physics):
// --- PHYSICS ---
const BASE_RING_SPACING = 300;
const ARTICLE_ORBIT_OFFSET = 80;
Replace with (Physics):
// --- PHYSICS ---
// Constants loaded from CONFIG object at top of script
Find (Radial Force):
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
// Aggressive offset: Push articles 60px further out than the Hub ring
if (d.group === 'article') return baseRing + 240;
return baseRing;
}, width / 2, height / 2)
Replace with (Radial Force):
.force("r", d3.forceRadial(d => {
const baseRing = d.depth * CONFIG.BASE_RING_SPACING * radialMultiplier;
// Aggressive offset: Push articles further out than the Hub ring
if (d.group === 'article') return baseRing + CONFIG.ARTICLE_OFFSET;
return baseRing;
}, width / 2, height / 2)
Find (Zoom Slider Logic):
// Slider -> Graph
zoomSlider.addEventListener("input", (e) => {
const val = parseFloat(e.target.value);
// Logarithmic feel for zoom
const targetScale = initialScale * Math.pow(1.02, val);
svg.transition().duration(50).call(zoom.scaleTo, targetScale);
zoomLabel.innerText = Math.round(Math.pow(1.02, val) * 100) + "%";
});
// Graph -> Slider (Sync on Scroll/Pinch)
zoom.on("zoom", (event) => {
g.attr("transform", event.transform);
const currentScale = event.transform.k;
const relativeScale = currentScale / initialScale;
if (relativeScale > 0) {
const val = Math.log(relativeScale) / Math.log(1.02);
zoomSlider.value = val;
zoomLabel.innerText = Math.round(relativeScale * 100) + "%";
}
});
// Initialize colors immediately
updateColors();
document.getElementById("status").innerText = "Simulation Running.";
// Re-heat the simulation to ensure the "Explosion" visual happens visibly
simulation.alpha(1).restart();
// --- APPLY INITIAL ZOOM (Deferred) ---
// We calculate and apply this NOW, ensuring the nodes exist and the simulation is active.
const initialTx = (width * (1 - initialScale)) / 2;
const initialTy = (height * (1 - initialScale)) / 2;
svg.call(zoom)
.call(zoom.transform, d3.zoomIdentity.translate(initialTx, initialTy).scale(initialScale));
Replace with (Zoom Slider Logic using CONFIG):
// Slider -> Graph
zoomSlider.addEventListener("input", (e) => {
const val = parseFloat(e.target.value);
// Logarithmic feel for zoom
const targetScale = CONFIG.INITIAL_SCALE * Math.pow(1.02, val);
svg.transition().duration(50).call(zoom.scaleTo, targetScale);
zoomLabel.innerText = Math.round(Math.pow(1.02, val) * 100) + "%";
});
// Graph -> Slider (Sync on Scroll/Pinch)
zoom.on("zoom", (event) => {
g.attr("transform", event.transform);
const currentScale = event.transform.k;
const relativeScale = currentScale / CONFIG.INITIAL_SCALE;
if (relativeScale > 0) {
const val = Math.log(relativeScale) / Math.log(1.02);
zoomSlider.value = val;
zoomLabel.innerText = Math.round(relativeScale * 100) + "%";
}
});
// Initialize colors immediately
updateColors();
document.getElementById("status").innerText = "Simulation Running.";
// Re-heat the simulation to ensure the "Explosion" visual happens visibly
simulation.alpha(1).restart();
// --- APPLY INITIAL ZOOM (Deferred) ---
// We calculate and apply this NOW, ensuring the nodes exist and the simulation is active.
const initialTx = (width * (1 - CONFIG.INITIAL_SCALE)) / 2;
const initialTy = (height * (1 - CONFIG.INITIAL_SCALE)) / 2;
svg.call(zoom)
.call(zoom.transform, d3.zoomIdentity.translate(initialTx, initialTy).scale(CONFIG.INITIAL_SCALE));
Would you like me to generate a new comprehensive blueprint summarizing these physics and configuration changes?
Me: Okay, that’s this plus a bit zooming in:
[mike@nixos:~/repos/trimnoir/_includes]$ vim show_graph.html
[mike@nixos:~/repos/trimnoir/_includes]$ git --no-pager diff
diff --git a/_includes/show_graph.html b/_includes/show_graph.html
index 1d1a729..4f64e52 100644
--- a/_includes/show_graph.html
+++ b/_includes/show_graph.html
@@ -94,7 +94,14 @@
<script>
(function() {
- const DATA_URL = "{{ site.baseurl }}/graph.json";
+ // --- 🎛️ CONFIGURATION ---
+ const CONFIG = {
+ DATA_URL: "{{ site.baseurl }}/graph.json",
+ INITIAL_SCALE: 0.15, // Set your default zoom here
+ BASE_RING_SPACING: 300, // Distance between concentric rings
+ ARTICLE_OFFSET: 240 // How far "out" fleas hug the hub
+ };
+
const container = document.getElementById('graph-container');
const width = container.clientWidth;
const height = container.clientHeight || (window.innerHeight * 0.7);
@@ -109,10 +116,8 @@
// Define behavior, but apply later
const zoom = d3.zoom()
.scaleExtent([0.05, 3]);
-
- const initialScale = 0.12;
- fetch(DATA_URL)
+ fetch(CONFIG.DATA_URL)
.then(response => {
if (!response.ok) throw new Error(`HTTP error! Status: ${response.status}`);
return response.json();
@@ -165,9 +170,9 @@
.strength(d => d.type === 'hub_link' ? 0.2 : 2.0))
.force("charge", d3.forceManyBody().strength(-200))
.force("r", d3.forceRadial(d => {
- const baseRing = d.depth * BASE_RING_SPACING * radialMultiplier;
- // Aggressive offset: Push articles 60px further out than the Hub ring
- if (d.group === 'article') return baseRing + 240;
+ const baseRing = d.depth * CONFIG.BASE_RING_SPACING * radialMultiplier;
+ // Aggressive offset: Push articles further out than the Hub ring
+ if (d.group === 'article') return baseRing + CONFIG.ARTICLE_OFFSET;
return baseRing;
}, width / 2, height / 2)
// Give articles maximizing strength (1.0) to enforce the ring position
@@ -273,11 +278,12 @@
const zoomSlider = document.getElementById("slider-zoom");
const zoomLabel = document.getElementById("val-zoom");
+ // Slider -> Graph
// Slider -> Graph
zoomSlider.addEventListener("input", (e) => {
const val = parseFloat(e.target.value);
// Logarithmic feel for zoom
- const targetScale = initialScale * Math.pow(1.02, val);
+ const targetScale = CONFIG.INITIAL_SCALE * Math.pow(1.02, val);
svg.transition().duration(50).call(zoom.scaleTo, targetScale);
zoomLabel.innerText = Math.round(Math.pow(1.02, val) * 100) + "%";
@@ -288,7 +294,7 @@
g.attr("transform", event.transform);
const currentScale = event.transform.k;
- const relativeScale = currentScale / initialScale;
+ const relativeScale = currentScale / CONFIG.INITIAL_SCALE;
if (relativeScale > 0) {
const val = Math.log(relativeScale) / Math.log(1.02);
@@ -306,11 +312,11 @@
// --- APPLY INITIAL ZOOM (Deferred) ---
// We calculate and apply this NOW, ensuring the nodes exist and the simulation is active.
- const initialTx = (width * (1 - initialScale)) / 2;
- const initialTy = (height * (1 - initialScale)) / 2;
+ const initialTx = (width * (1 - CONFIG.INITIAL_SCALE)) / 2;
+ const initialTy = (height * (1 - CONFIG.INITIAL_SCALE)) / 2;
svg.call(zoom)
- .call(zoom.transform, d3.zoomIdentity.translate(initialTx, initialTy).scale(initialScale));
+ .call(zoom.transform, d3.zoomIdentity.translate(initialTx, initialTy).scale(CONFIG.INITIAL_SCALE));
simulation.on("tick", () => {
link.attr("x1", d => d.source.x).attr("y1", d => d.source.y)
[mike@nixos:~/repos/trimnoir/_includes]$
Okay, there is still instances of articles “inside” the hubs where I guess the forces of the force graph push them so, and I believe that’s because articles live at the same level as their parent hubs. But for now this is definitely achieving the 80/20-rule. The few instances of articles inside the hubs is far outweighs by the “fleas on the back of the hub” look that’s created in most places. So we’ll cut the article here, bank it and have Gemini wrap it up.
Respond by expanding on this article. Don’t just stay in abstract terms; anchor your points in hard reality. Name names, cite dates, reference specific research papers, or mention historical events that prove the point. Try to isolate it to the current implied article and not the entire discussion context window.
Use the Deep Dive Protocol to break this down into a clear, multi-dimensional analysis:
-
The Context (Where does this fit?): Don’t just label it; locate it in the real world. Is this a new idea or an old one with a new coat of paint? Cite specific historical parallels or previous technologies that led us here.
-
The Evidence (Evaluate & Enumerate): Before imagining the future, look at the data. Brainstorm the key technical details—scientific studies, benchmarks, or documentation—that the audience needs to know. Don’t assume they know it; teach them with facts.
-
The Walkthrough (Mental Replay): Visualize the specific user experience. What does it feel like to actually do this? Describe the friction, the “aha!” moment, and the flow. Make the abstract concrete.
-
Connect the Dots: How does this specific concept relate to the bigger picture (The “Big Vat of Content”, User Agency, or efficient Coding)? Show the relationship between this small piece and the whole system.
-
The Reality Check (What If?): Run the scenario. What happens if this tool/insight didn’t exist? What is the cost of doing it the “old way”? Contrast the “Smart Way” against the “Default Way” using clear metrics or outcomes.
-
The Verdict: Is this actually useful or just hype? Is it fuel for the engine or just sugar? Give a clear, honest assessment supported by the evidence in step 2.
Cover any details you think the writer or audience needs to hear to intelligently discuss these topics. Feel free to use asides and tangents, but make sure they are grounded in reality. Mention what surprised you most and what you anticipate next.
Gemini 3 Pro: ### The Physics of Context: Engineering the “Flea” Effect in D3.js
The visual reorganization of your link graph isn’t just an aesthetic tweak; it is a fundamental shift in how we map information hierarchy. We moved from a rigid, stratified model to a gravity-biased clustering model. This analysis breaks down the move from “loose orbits” to the “flea on the back of the hub” visualization, where articles tightly hug their parent topic while remaining distinct.
1. The Context: From Hierarchies to Force Fields
Historically, web navigation has been dominated by the Tree Structure, a concept formalized in computer science by nodes and edges, famously implemented in file systems (UNIX, 1969) and the DOM. In a traditional tree, children sit “below” parents.
However, Mike Bostock’s D3.js (Data-Driven Documents), released in 2011, introduced a physics-based approach to visualization using Verlet Integration. This simulates physical forces—gravity, charge, and collision—to find a “low energy” state for the layout.
Your challenge was a classic Map-Territory Relation problem (Alfred Korzybski, 1931). Your data (the Map) said “Articles are children of Hubs.” But your desired visualization (the Territory) wanted articles to act like texture or satellites hugging the surface of the Hub, not distant planets orbiting it.
1. The Context: From Hierarchies to Force Fields
2. The Evidence: The Conflict of Forces
To achieve the “Flea” effect, we had to resolve a conflict between three mathematical forces operating in d3-force:
forceRadial: Pushes nodes to a specific radius based ond.depth.forceLink: Pulls connected nodes together (Hooke’s Law).forceCollide: Prevents nodes from overlapping (hard boundaries).
The Data:
In the previous graph.json, articles had depth: 2 and Hubs had depth: 1.
- Result:
forceRadialpushed articles to the “Ring 2” orbit (600px), whileforceLinktried to pull them back to “Ring 1” (300px). They were being ripped apart, resulting in the “loose” layout.
The Hack:
We modified build_knowledge_graph.py to assign articles the same depth as their parents.
- New Reality: Both Hub and Article compete for “Ring 1.”
- The Visualization Tweak: In
show_graph.html, we injected a targeted bias:if (d.group === 'article') return baseRing + 240;.
This creates a distinct “Micro-Orbit.” The Hub sits at 300px. The Article wants to sit at 540px (300 + 240), but the forceLink (set to a tight 20px distance) acts as a leash. The result is high-tension clustering: the “flea” effect.
2. The Evidence: The Conflict of Forces
3. The Walkthrough: A Developer’s flow
- The Observation: You load the Jekyll site. The graph explodes outward. The articles are drifting too far into the void, disconnecting them visually from their context.
- The Diagnosis: The
forceRadialis overpowering theforceLink. - The Pivot: You edit
build_knowledge_graph.py. You explicitly flatten the hierarchy: ` “depth”: depthinstead ofdepth + 1`. This effectively “demotes” the articles from being children to being siblings in the eyes of the physics engine. - The Fine-Tuning: You open
show_graph.html. You move the configuration to the top (CONFIG.ARTICLE_OFFSET). You aggressively dial the offset to240. - The Result: You refresh. The physics engine re-heats. The nodes fly out, but instead of drifting, the articles snap back, hugging the outer rim of the Hubs. They are “outside” but “attached.”
3. The Walkthrough: A Developer’s Flow
4. Connect the Dots: Information Density
This specific visualization technique connects directly to the concept of High-Bandwidth Communication.
- The Big Vat: In a flat list (blog archive), context is lost.
- The Graph: Restores context. By clustering articles tightly (fleas) around the Hub (dog), a user can instantly judge the “weight” or “density” of a topic. A Hub with 50 tightly packed fleas is visibly different from a Hub with 2.
- User Agency: This allows the user to navigate by mass rather than just chronology. They can see where you have spent your energy.
4. Connect the Dots: Information Density
5. The Reality Check: The Cost of “Truth”
What if we kept the “correct” data structure (Depth + 1)?
- The Default Way: The graph would look like a standard corporate org chart wrapped in a circle. It implies distance and separation.
- The Problem: On a mobile device or small screen, that separation forces the user to zoom out so far that the labels become unreadable.
- The “Smart” Way (Current): By “lying” to the physics engine (flattening depth) and using a visual offset, we condense the information. We sacrifice strictly accurate orbital rings for semantic proximity.
Metric of Success: The “80/20 Rule” applies here. 80% of the nodes now exhibit the desired behavior (tight external hugging), creating a coherent visual structure that outweighs the 20% of edge cases (internal overlaps) caused by the chaotic nature of force simulations.
5. The Reality Check: The Cost of “Truth”
6. The Verdict: Fuel for Intuition
This visualization strategy is Fuel.
It is not merely “sugar” (eye candy). It converts abstract metadata (parent-child relationships) into intuition. When a visitor looks at the graph, they don’t read the connections; they feel the gravity of the topics.
Surprising Insight: The most effective way to visualize a hierarchy in a force-directed graph was to mathematically remove the hierarchy (flatten the depth) and re-introduce it as a visual bias (offset). Sometimes you have to break the data model to save the mental model.
What’s Next: The natural evolution is Interaction. Now that the “fleas” are tight, hovering over a Hub should perhaps highlight all its fleas, or clicking a flea should rotate the entire system to bring that cluster to the foreground (The “Exploding Graph” concept).
6. The Verdict: Fuel for Intuition
Next Step
Would you like me to analyze the current update_graphs.py pipeline to ensure this new data structure (flattened depth) is robustly preserved during automated updates, or should we focus on the next visual iteration (e.g., color-coding the fleas based on velocity)?
Me: No, I know
update_graphs.pyis working. And I’m not really even sure next steps. I think this brought it to a nice resting point as we go into the formal work-week.
Book Analysis
Ai Editorial Take
This piece is an excellent deep dive into the practical challenges of data visualization, particularly within the D3.js ecosystem. It perfectly illustrates the critical distinction between fixing a problem at the data source (architectural) versus applying a cosmetic patch at the display layer. The iterative dialogue and eventual solution of adjusting the depth attribute in the Python script, combined with precise D3.js force tuning, make this a highly valuable resource for anyone building dynamic knowledge graphs. It serves as a compelling case study for the ‘Age of AI’ where precision in data representation directly impacts user understanding and interaction.
Title Brainstorm
- Title Option: Mastering D3.js Force Graphs: The ‘Flea’ Effect Visualization
- Filename:
mastering-d3js-force-graphs-flea-effect-visualization.md - Rationale: Clearly states the technology, the specific visual goal, and the outcome, focusing on the refined visualization.
- Filename:
- Title Option: D3.js Flea Effect: Architectural Purity vs. Visual Pragmatism
- Filename:
d3js-flea-effect-architectural-purity-visual-pragmatism.md - Rationale: Highlights the core tension and resolution between data logic and display adjustments.
- Filename:
- Title Option: Engineering Semantic Proximity in D3.js Knowledge Graphs
- Filename:
engineering-semantic-proximity-d3js-knowledge-graphs.md - Rationale: Focuses on the user experience and the semantic goal of the visualization.
- Filename:
- Title Option: The Micro-Orbit: Fine-Tuning D3.js Force Layouts for Intuitive UX
- Filename:
the-micro-orbit-fine-tuning-d3js-force-layouts-intuitive-ux.md - Rationale: Emphasizes the technical detail of the ‘micro-orbit’ and its user benefit.
- Filename:
Content Potential And Polish
- Core Strengths:
- Illustrates an iterative problem-solving approach in D3.js visualization.
- Clearly delineates the difference between data-level and display-level fixes.
- Provides practical code examples and a refactored configuration block.
- Anchors technical solutions in user experience and information architecture principles.
- Offers a detailed walkthrough of debugging D3.js force conflicts.
- Suggestions For Polish:
- Include visual diagrams or animated GIFs of each iteration (before, during, and final state) for better comprehension.
- Discuss potential performance implications of force simulations on very large datasets and strategies for optimization.
- Expand on the ‘Exploding Graph’ concept, perhaps outlining a plan for its implementation as a future feature.
- Add a brief introductory section on D3.js force-directed graphs for readers less familiar with the framework.
Next Step Prompts
- Develop a follow-up article detailing the implementation of ‘The Exploding Graph’ concept, where clicking a hub dynamically re-centers and expands its cluster for focused exploration.
- Create a guide for optimizing D3.js force-directed graphs for performance on large knowledge bases, including strategies for Web Workers or pre-calculated layouts.
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