Graph

What it drawsCopy Anchor Link

A node-link diagram of a levelled directed graph: every node sits in a column determined by its distance from the root, and edges curve between columns. Two kinds of result draw here.

An assembly plan is the commonest: each node is a DNA part or an intermediate construct, each edge is an assembly step that consumes its sources and produces its target, and the columns are assembly rounds. Reading left to right is reading the order in which you would do the cloning at the bench — everything in column two can only be built once column one exists.

A provenance lineage draws the same way over a different relation: a node is a document or a file, and an edge means "this was derived from that". The columns are generations, so the leftmost column is what you started from and the rightmost is what you have now.

Node position is not a cosmetic layout. It is computed by the same levelled-graph geometry that the assembly-planning literature uses for these figures, so a plan drawn here has the shape it would have in a published methods figure rather than the shape a generic tree layout would give it.

What opens in itCopy Anchor Link

Nothing is opened here from a file. This canvas is the picture of a result computed in the editor — an assembly plan produced by a cloning simulation, or the lineage assembled from a project's own history.

A phylogeny does not draw here even though it is also a graph: a tree has its own canvas, with rooting, ladderization and branch-length scales that a levelled DAG has no meaning for. A pairwise sequence comparison is a dot plot, not a graph.

What this computesCopy Anchor Link

The plan or the lineage is computed by the tool that produced it. What this canvas computes is the geometry, and on a levelled graph the geometry carries meaning that a generic tree layout would destroy.

• A level for every node, from its distance to the root. That level is the column, so the horizontal axis is depth in the dependency relation and nothing else.
• The reading that follows from it: for an assembly plan, a column is an assembly round, and everything in column two can only be built once column one exists. For a provenance lineage, a column is a generation, leftmost being what you started from. Columns are levels, not time stamps — two nodes in one column are at equal depth, not necessarily done on the same day.
• Edge routing between columns, drawn source → product, left to right. A node with several incoming edges is a multi-input assembly, which is the normal case rather than an error.
• Nothing else. A levelled graph has no free parameters once its levels and edges are fixed, so there is no scale to set and none is offered; adjusting it could only misrepresent the plan.

No shade on this canvas encodes a quantity. Colour is a role — the final construct distinguished from intermediates, so the endpoint of a multi-round plan is findable at a glance — which means nothing is lost by reading this canvas in grayscale.

Reading itCopy Anchor Link

Columns are levels, not time stamps. Two nodes in the same column are at the same depth from the root; they are not necessarily done on the same day, and nothing says they are independent of each other in the lab.

Edge direction is source → product, drawn left to right. A node with several incoming edges is an assembly with several inputs — that is the normal case for a multi-fragment assembly, not an error.

The label inside a node is the part or document name; hovering adds the secondary line, which carries the facts that distinguish two similarly named parts, such as a length and an enzyme.

Colour here is a role, never a measurement: the final construct is distinguished from intermediates so the endpoint of a multi-round plan is findable at a glance. No shade on this canvas encodes a quantity, so nothing is lost by reading it in grayscale.

ControlsCopy Anchor Link

The drawing has no scale to set: a levelled graph has no free parameters once its levels and edges are fixed, so there is nothing to adjust that would not misrepresent the plan.

Hovering a node raises its detail; that is the one interaction, and it is the disclosure of facts already in the result rather than a change to the drawing. When the diagram is shown as a preview rather than as a full tab, the hover detail is still available — the preview is smaller, not poorer.

Where it appearsCopy Anchor Link

As a stage tab, when a planning tool hands its result to the canvas; and inside the panel that produced it, at panel width. The geometry is identical in both — only the pixel box changes, because the layout is computed in a unit square and mapped to whatever room it is given.

Performance and limitsCopy Anchor Link

Two limits are worth knowing before you read a large plan. A graph whose columns are very deep will compress vertically rather than scroll, so node labels are the first thing to become unreadable — that is the signal to read the plan from the panel's table instead, which carries the same steps as rows. And a levelled layout says nothing about crossing minimisation: edges may cross where a hand-drawn figure would route around, and a crossing carries no meaning.

ScreenshotsCopy Anchor Link

No frame is committed for this canvas yet. What one would show: an assembly plan or a workflow DAG drawn as columns by distance from the root.

The absence is stated rather than left as a blank heading: a picture that does not exist yet is worth knowing about, and a placeholder would be worse than either.

RelatedCopy Anchor Link

The cloning-simulation and assembly-planning tools write to this canvas; the provenance surface writes the lineage form of it.