The Graph

Press ⌃⌘G — or click Graph in the toolbar — and your document becomes a living map: every page a node, every link an edge, arranged by a gentle physics simulation.

The Graph's controls live in a single stack down the left edge of the canvas — find, fit, the overlays, the pickers, all of them, one under the next at one width. Nothing hides in an overflow on a small screen: a MacBook Air sees exactly what a big display sees.

How the Graph looks — Cosmos, Dots, or Off

On a dark theme the Graph renders as a living cosmos: pages glow as soft stars, links curve as luminous filaments with light flowing along them, and the whole map breathes over a faint starfield. Open or select a page and a pulse of light races outward along its connections — you watch an idea radiate to everything it touches. Turn on Territories (below) and each one is drawn as a real constellation, its pages joined by star-lines and its AI name floating above a glowing nebula. On the Timeline (below) each page flares to life as you scrub — your wiki forming like a time-lapse galaxy.

That cosmos is for dark themes. On a warm, light theme — Parchment, Sepia, Linen — the Graph dresses differently: an illuminated manuscript of ink-stroke links and ink-wash nodes, with soft watercolor washes behind your territories, all on paper.

The theme picker at the bottom of the Graph's control stack gives the Graph its own look — independent of your app theme, colouring the Graph only, not your pages. Alongside the classic colour palettes (Midnight, Cobalt, Matrix, and the rest) it offers nine animated themes, each alive with its own kind of motion:

• ✦ Cosmos — the full animated galaxy (the default).
• Synapse — a neuron net on deep navy; signals fire down the links as you navigate.
• Thermal — a live heatmap, nodes coloured by how recently you touched them (hot → cool).
• Phosphor — a radar screen, a green sweep pinging each node as it passes, with scanlines.
• Aurora — drifting curtains of teal and violet across the void.
• Noir — high-contrast black & white with a spotlight that follows your focus.
• Cartography — an explorer's parchment map with inked nodes and contour lines.
• Metro — a clean transit map: stations joined by coloured lines.
• Mycelium — a dark cave of bioluminescent threads and glowing spores.

The same picker holds the calmer looks too — · Dots (simple lines and moving dots, no glow) and ⏸ Static (no animation, for when motion is distracting). Your choice is remembered, and MojoPad honors your Mac's Reduce Motion setting (System Settings ▸ Accessibility ▸ Display) — with no choice saved yet, the Graph opens calm.

• Size — the more connected a page, the larger its node. Your hubs are obvious at a glance.
• Hover a node to light up its neighborhood; everything else fades.
• Find — type in the field at the top-left and matching nodes light up while the rest dim; Return previews the best match. The ⊙ button (or double-clicking the background) re-fits the whole graph in the window.
• Click a node and the page appears in a preview pane on the right — the graph stays up, so you can keep exploring. Page links inside the preview move the preview (and the ring in the graph) to that page, and the ‹ › buttons in the pane header retrace your exploration. Drag the pane's left edge to resize it (double-click the divider to reset); the width is remembered.
• Double-click a node — or ⌘-click it, or press Open Page in the preview — to leave the graph and really go there.
• Drag nodes to untangle; drag the background to pan; scroll to zoom. Esc closes the preview pane first, then the graph.
• Big documents — past a few hundred pages, the graph opens on the neighborhood of the current page (everything within two links) instead of an unreadable thousand-node tangle. A button beside Find swaps between the neighborhood and the whole document; on the whole-document view, labels appear as you hover or zoom in.

Reading a node at a glance

Nodes carry more than position. A page with a type glows in that type's colour (see Page Types); a page with an emoji icon wears it on its node; a page with a cover image shows a small circular thumbnail of that cover — so your important pages are recognisable without reading a single label. And with an embedding model present, MojoPad writes each page a one-line summary: hover a node and its gist appears beside the name, so you can survey a whole region without opening anything. The same summary heads the preview pane.

A legend for the map

A faint key sits in the bottom-left corner — it brightens when you hover. A solid line is a link you made; a dashed cyan line is an AI-spotted relationship you haven't linked; and coloured dots are Page Types. (The page-type row only appears once you've made some.)

A living canvas

The graph isn't a static diagram — it breathes. A gentle, continuous motion keeps clusters legible; edge particles drift along the busiest links to show the flow of connection; the page you're previewing carries a soft focal glow that ripples out to its neighbours; and a faint depth vignette settles the whole thing into the window. It's meant to feel less like a chart and more like a place you can sit in and think.

Focus — travel your wiki as a plex

The whole map at once is a beautiful thing to look at, but past a few dozen pages it's a lot to use. Click ◎ Focus and the Graph becomes a place you navigate instead: the page you're on glides to the centre, its immediate relationships fan out around it, and everything else fades to faint context.

Where a neighbour sits tells you the relationship — you don't have to read anything:

• ↑ Backlinks above — pages that link to this one (where the idea came from).
• ↓ Outgoing links below — pages this one links to (where it leads).
• ← Connections to the left — links you drew by hand.
• AI suggestions → to the right, drawn as dashed cyan lines — pages that are related by meaning but you never linked them, surfaced by the local model. The hidden links you'd never have drawn yourself.

Faint labels at the edges name each zone, so the layout explains itself. And the light streams down through the page you're on — backlinks pouring in from above, outgoing links flowing out below — so you can feel the inflow and outflow, not just see it. (The dashed AI suggestions don't stream; they're potential connections, not active flow.)

Click any neighbour and it becomes the new centre — its own neighbours fan out and you keep going, page by page, following a thread. A breadcrumb trail (marked with a ⤳) builds across the top as you travel; click any step to walk back. Click ◎ Focus again to drop to the full map.

The AI suggestions need an embedding model (see Local AI). Focus is the second-brain way to think with your map instead of just looking at it.

Make a map by hand

The graph isn't only a picture you read — it's a canvas you can shape:

• Drag a node onto another to link the two pages — a real connection you'll see in Backlinks and on the map.
• ⌥-drag one node onto another to merge them — MojoPad folds the first page's content into the second, repoints every link that pointed at either, and clears away the leftover.
• Double-click empty space to create a new page right there, already placed where you dropped it.
• Gather — hold ⇧ and drag a box around a cluster of nodes, then choose: spill them as cards on a canvas (a board to arrange and connect — see The Canvas), or pull them into a fresh Map of Content: a new page that links to everyone you boxed in.

Territories — your themes, named

Click ◇ Territories and MojoPad groups related pages into glowing, labelled regions — the natural themes of your wiki, found by meaning and named by the local model. Suddenly you can see what your document is about, not just how it's wired.

• ⌘-click a territory to spin up a Map of Content for it — a page that gathers and links everything in that theme.
• Explain — ask why a region was grouped and named the way it was; the reasoning streams in, grounded in the real page names.
• Rename — disagree with a name? Type your own and it sticks to that region from then on.

Territories need an embedding model (see Local AI), and they're sharpest on a wiki with some substance — a handful of pages won't cluster into meaningful themes, so MojoPad would rather show none than a grab-bag.

A timeline of your thinking

Flip on ◷ Timeline to colour every node by recency — fresh pages glow, old ones cool — and drag the scrubber to replay your wiki growing, page by page, from its first note to today — the ½×–4× control sets how fast it plays.

Lenses and paths

Two more ways to read the structure:

• Lens — the Lens… menu spotlights the pages that share one trait, lighting them up while everything else dims. By Page type, your colour-coded categories (see Page Types); by tag, any tag, so you can see where it lives and where it's missing; by format, rich text, Markdown, plain text, or attachments. The honest answer to “where is all my X?”.
• Path — click → Path, then two nodes, and MojoPad lights up the shortest chain of links between them — the trail of pages that connects one idea to another. The honest answer to “wait, how are these two even related?”

Take a poster home

Click ⤓ Poster in the graph toolbar and MojoPad renders the view you're looking at — same camera, same theme — as a high-resolution image, stamped quietly in the corner with the document's name and the date. It saves wherever you choose, ready to share, print, or set as a wallpaper. The poster is a photograph of this moment in your thinking: export one now and again and you get a time-lapse of your wiki growing up.

Trails — the desire paths of your thinking

Parks planners know the truth about footpaths: people walk where they need to go, and the grass remembers. Click ⋱ Trails and MojoPad draws the same thing on your map — the routes you actually travel between pages, worn in as dotted amber footpaths. The links you declared show where you thought the roads should be; the trails show where you really walk. A route you take daily burns bright and wide; one you took twice last month is a faint track; a path you stop walking grasses over and fades from the map within a few weeks. (Trails are drawn over the terrain without disturbing it — they never pull pages around.)

The interesting moment is a well-worn trail where no link exists — your habits found a road your wiki never built. Turn Trails on and MojoPad points at the hottest one: you've walked between these pages 14 times, but no link exists. Pave it turns the trail into a real connection (the same curated connection the Connect button makes — no page text is touched), or Let it grass over clears the trail; it only returns if you keep walking the route. Click any trail on the map for the same choice.

How it counts: moving from one page to another within a few minutes of each other wears the trail between them one step deeper, whichever direction you walked. Trips are remembered in the document's attention file — ids and timestamps only, never content — and decay on a gentle half-life, so the map always shows your current habits, not a fossil record.

Film your wiki growing up

The Timeline's ▶ has always replayed your wiki's growth — every page flaring to life in the order you created it. Now press ⏺ Film and MojoPad records the whole replay straight off the canvas and saves it as a video: your year of thinking as a twenty-second time-lapse, territories forming like weather systems. Pick a playback speed first to set the film's length. It's the single best way to show someone what a living wiki feels like.

The Atlas — a map that scales with your wiki

A five-hundred-page wiki drawn as five hundred dots is a hairball, so past a few hundred pages the graph becomes an atlas. Territories switch on automatically, and the map changes with your altitude the way a real map does: zoomed out, your themes render as named landmasses — each showing how many pages live there — joined by a few bundled routes whose thickness is how much traffic of links flows between those two worlds. Only each region's anchor pages stay visible as stars. Glide in and the region resolves — first its hubs, then every page and edge, exactly as before. Nothing is hidden from search, Focus, or the lenses; the atlas only changes what's drawn at a distance, so the map stays legible at any size — and honestly, gets better the bigger your wiki grows.

The Garden — five unhurried minutes on the map

Choose ✦ AI ▸ ✂ Garden and the map becomes a short, bounded tidy-up — one card at a time, with a visible end. Orphans drift gently to a nursery row at the map's edge, each offering the page it reads closest to: Plant it there (one connection, no page text touched), Leave wild (a deliberate loner — never asked about again), or Compost (off to Recently Deleted, undoable). A brittle bridge — one page holding a whole region on — asks for a second road. A fading page offers itself for watering: read it for a minute and the memory trace freshens. Skip anything; the session ends with an honest count. Gardening a wiki used to be a chore list — now it's the most pleasant thing you'll do on the map all week.

Load-bearing pages — the columns holding the roof

Some pages quietly hold your wiki together: remove one and a whole neighborhood breaks away from the rest. Pick Lens ▸ 🏛 Load-bearing pages and MojoPad finds them with honest graph math (no AI involved) — each keystone lit on the map and listed with how many pages it holds onto the rest. If one column carries too much, Build a second road adds one curated connection around it, choosing the best match by meaning — so losing (or archiving) that page one day would no longer orphan everything behind it.

Strange bridges — what you didn't know you knew

Choose ✦ AI ▸ Strange bridge and the graph hunts for the most surprising connection you own: two pages that read as completely different worlds to the meaning index, yet sit only two or three links apart. The route lights up on the map — sourdough to Kubernetes by way of your weekly schedule — and your local AI names the hidden thread in one sentence. Surprise me again keeps going; every bridge is shown once before the tour repeats. It's the inverse of search: not "find me this," but "show me something I didn't know I knew." (Needs the meaning index — see Local AI.)

Your memory as a landscape

The graph knows how well you remember what's on it — see Remember — Spaced Repetition for the machinery. Three views come of it:

• 🎴 Memory Map (Lens ▸ Memory) paints every page that carries flashcards by the live recall probability of its cards — strong knowledge glows green, fading cools through amber to red, untested sits grey. The legend adds a 30-day forecast (“without review, ~14 cards fade”) and a one-click Review the fading pages.
• 🌒 Fading knowledge (same menu) does it for the whole wiki, cards or not: every visit or edit strengthens a page's trace, time fades it — so the map shows where your attention still lives and where it's drifted. Bright where you work, dark where you've forgotten.
• 🌊 The Undertow (toolbar) is the one that feels like magic: from the page you came from, threads of light reach across the dimmed map to old notes related to your current thought — the faded-but-relevant, ranked by meaning × how far they've slipped. A panel lists them with last-touched dates; Bring them back reopens them in tabs. Notes you wrote years ago rejoin the thought you're having today.

To try them: open the page you're working on, press ⌃⌘G for the graph, and click 🌊 Undertow in the toolbar — the threads draw from that page. (If nothing lights up, its neighbourhood is still fresh in memory — the panel says so.) The two lenses live in the Lens… menu under Memory; picking Lens… again clears them, and clicking Undertow a second time turns it off. The Undertow reads best with an embedding model installed (see Local AI); without one it falls back to linked neighbours.

Ask, command, and converse

The ✦ AI… menu in the graph toolbar is where the local model goes to work on your map:

• Ask or command opens Chat with your wiki — a real, multi-turn conversation grounded in your own pages. Ask a question and the answer streams back with the pages it drew from as clickable source chips that light up on the map. Follow-ups keep their context, so “tell me more about the third one” just works. The same box also understands commands — “show me what changed last week”, “path from A to B”, “find duplicates” — and drives the map instead of answering in prose. ⟲ starts a fresh conversation.
• Explain this graph — a plain-language read of what your wiki is mostly about, how connected it is, and what's being neglected.
• Find issues to fix — the health view; see below.
• Suggest links and Suggest pages to create — the model proposes connections worth making and pages worth writing, from the shape of what you already have.
• Build an index — generate a Map of Content for the whole document, or a slice of it.

Everything here is local and grounded: answers come from your pages, with sources, and nothing is sent anywhere.

Keeping your wiki healthy

The Graph button in the toolbar wears a small badge when your wiki has loose ends worth tending. Click through to ✦ AI ▸ Find issues to fix for the breakdown, each item with a one-click fix:

• Likely duplicates — pages that read almost identically, each with a Merge button.
• Orphans — pages with no links in or out. For each one MojoPad finds the nearest page by meaning and offers a Link → button, so an orphan rejoins the conversation in a click.
• Untagged — pages with no tags, each with a Tag button that asks the model for a few, reusing your existing tag vocabulary.

A one-line summary up top — pages, percent linked, orphans, duplicates, untagged — tells you the shape of things at a glance. (On a wiki of mostly stand-alone clippings the orphan count can run high; that's honest, not alarming.)

Connections, suggestions, and why

Below the page in the preview pane is a Connections list — everything this page links to, every page that links back to it, and any connections you've drawn by hand. Under that, Suggested lists pages that read like this one but aren't linked yet (this one needs an embedding model — see Local AI). Every row carries:

• Why? — MojoPad reads both pages and explains, in a sentence or two, how they relate. The explanation streams in right under the row, and it's entirely local.
• Connect — promote a suggestion to a real connection: it jumps up into Connections and draws an edge in the graph.
• Disconnect — remove a connection you made by hand.
• Unlink — for a page MojoPad links to or that links here, prune the connection. It's made for auto-links: when a page's name turns up in another page that doesn't really relate, Unlink records a permanent exclusion so the two never auto-link again. (A link you typed by hand is left in place — MojoPad points you to the page so you can remove it yourself.)

Prefer the map itself? Toggle ◌ Semantic at the top-left to lay dashed “these read alike” lines over the whole graph — the slider beside it sets how alike is alike enough — with a live count of the links it's drawing, so you watch them thin out as you raise the bar. Click any edge, solid or dashed, for that same Why? explanation in a card, with a button to connect or disconnect the pair.

Connections by meaning. The lines on the map aren't only the links you typed — MojoPad also draws the connections it finds by meaning, reading what your pages are actually about (your local model, plus the distinctive words and tags they share). Each is graded deep, medium, or low by how related the two notes really are, and drawn boldest for the strongest; the ◆ Deep / Deep + medium / All control in the toolbar sets how far down you want to see. Click any meaning line for the same Why? card — or to make it a permanent connection. Because these come from meaning rather than a matching word, a common word in a title no longer wires unrelated notes together.

Territories — your real topics, named

Turn on ◇ Territories and MojoPad groups the map into glowing, named regions — your actual topic clusters. It finds them by community detection over the meaning connections (so the number of regions emerges from your wiki, not a fixed guess), and names each from the distinctive concepts its pages share, with your local model sharpening the label. Click a region's name to focus it; ⌘-click to spin a Map of Content page that gathers its members. A name you set by hand always wins — double-click to rename — and your names stick.

Explore beyond your wiki

The map shows what you've written — Explore reaches past it. Open a page in the plex (the preview pane where Focus and clicks land) and, at the bottom, ✦ Explore suggests real external articles on its subject: your local model distills the page into searches, runs a genuine web search, and curates the most relevant results — each with a line on why it connects. It works with no setup (Wikipedia, Hacker News, arXiv); add a Brave or SearXNG key under Settings ▸ Explore for broader results.

For any result, ⊙ Preview & decide renders the article in-app so you read it without leaving MojoPad — optionally ✦ Clean up (the model strips the nav and ads while keeping the article's own images and links) — then Save to wiki. Saved pages link back to the one you explored from, anything already clipped is marked so you don't grab it twice, and if the Graph is open the new note springs into the map as you save it.

The graph is honest cartography of how you actually think: tight clusters are your projects, bridges are your themes, and lonely dots at the edge are pages waiting to be linked into the conversation.