Transmission Chain View
⚠️ Feature in development: This feature is in development and is not yet available on the main MicrobeTrace site.
Transmission Chain View arranges connected records on a timeline so that links can be read together with the dates associated with their nodes. Each node's horizontal position comes from a selected date field. The vertical arrangement can either use MicrobeTrace's automatic cluster and connected-component grouping or a categorical node field such as state, facility, ward, or outbreak.
The view uses the node colors, node shapes, link colors, and other styling already configured in MicrobeTrace. It changes the layout of the data; it does not calculate or infer who transmitted an infection to whom.
| View element | What it represents |
|---|---|
| Horizontal position | The value in the selected Date Field. Earlier dates appear on the left and later dates appear on the right. |
| Horizontal axis | The time range covered by the visible dated nodes. |
| Vertical position | Automatic cluster and connected-component grouping, or the category selected under Y-Axis Field. |
| Colored node | A person, sample, place, or other record, using the current node styling. |
| Connecting line | A link from one of the selected Link Lists, using the current link styling. |
| Red number in the toolbar | The number of nodes omitted because the selected date field is blank or invalid. |
For the most useful result, load:
- Node data containing a unique identifier and at least one date field.
- One or more link lists describing relationships between nodes.
- Optionally, a categorical node field for vertical bands, such as
State,Facility,Ward, orOutbreak.
The date values must be valid dates that MicrobeTrace can interpret. Nodes without a valid value in the selected date field are not placed on the timeline.
- Load the node and link data, then launch the visualization.
- Open the View menu.
- Select Transmission Chain View.
- MicrobeTrace opens the view in a dedicated tab. If no date field has been selected yet, Transmission Chain View Settings opens automatically.
Open Settings, then select the Layout tab.
- Under Date Field, select the node field that should position nodes from left to right. In the sample dataset, select Date of symptom onset Date.
- Under Y-Axis Field, choose how to arrange nodes vertically:
- Select None to let MicrobeTrace separate clusters and connected components automatically.
- Select a categorical node field to create labeled horizontal bands. In the sample dataset, select State.
- Under Link Lists, select the imported link sources that should be drawn and used to arrange the chain. All link lists are selected by default.
- Select Select All to restore every available link list.
- Select Clear to show the dated nodes without links.
- Adjust Y Spacing to increase or decrease the vertical distance between nodes and bands.
- Close the settings panel. Select Center Screen in the view toolbar if the result needs to be fitted to the available space.
Changes are applied immediately, so the visualization behind the settings panel updates as each choice is made.
In the configured sample view:
- Dates progress from left to right along the bottom axis.
- State names label the horizontal bands.
- A node stays aligned with its date even if it is dragged vertically.
- When a Y-axis field is selected, a dragged node remains inside its category band.
- Hovering over a node or link displays its tooltip.
- Node and link colors retain their meanings from the other MicrobeTrace views.
The links show the relationships supplied in the selected link lists. Date order and visual proximity alone do not prove transmission direction or causality; interpret them together with the source data and the investigation context.
To change how connections are routed:
- Open Settings.
- Select the Network tab.
- Open Display.
- Choose a Line Style:
- Stepped is the default and draws right-angled source-stem paths.
- Straight draws direct lines between endpoints.
- Curved draws smooth curved connections.
- Fan-out Curves separates connections that share an endpoint, which can make crowded branching patterns easier to follow.
The Display section also controls neighbor highlighting and gridlines.
Each imported link source appears as a checkbox under Layout > Link Lists. Use these controls to compare different relationship sources without reloading the data.
- Selecting a link list adds its links to the view and includes them in the layout.
- Clearing a link list removes only its links; dated nodes remain visible.
- Clearing every link list produces a node-only timeline.
- When one relationship belongs to more than one selected link source, MicrobeTrace can display the combined relationship with solid and dashed link styling.
- Use the mouse wheel or trackpad to zoom.
- Drag the background to pan.
- Drag nodes vertically to separate overlaps. Their horizontal date position remains fixed.
- Select Center Screen to fit the current timeline and Y-axis layout in the view.
- Use the Nodes and Links settings tabs to change the same styling options available in 2D Network View.
- Select Export Screen to export the displayed visualization.
After a date field is selected, the red number in the view toolbar reports how many nodes do not contain a valid value for that field. Select the number to open Excluded Nodes and review the omitted records by index and ID.
Correct the source values or select a more complete date field if those records should appear in the timeline.
Saving the project as a .microbetrace session preserves the Transmission Chain View and its selected date field, Y-axis field, link lists, line style, and spacing. When an older session used the 2D Network timeline layout, MicrobeTrace migrates that layout to Transmission Chain View when the session is opened.
- Treat the horizontal axis as time associated with the selected node field, not as proof of transmission order.
- Treat links as relationships present in the selected source files. Their epidemiological meaning depends on how those files were created.
- Use a Y-axis field only when its categories are meaningful for the question being investigated.
- Compare link lists separately when genetic, contact, proximity, or other relationship sources have different meanings.
- Review excluded nodes before interpreting gaps in a chain.
- The view is blank: Open Layout and select a Date Field containing valid dates.
- Some nodes are missing: Select the red number in the toolbar. The listed nodes have blank or invalid values in the selected date field.
- No links are visible: Confirm that at least one item is selected under Link Lists and that the link endpoints match loaded node IDs.
- The view has no labeled horizontal bands: Select a categorical field under Y-Axis Field. None uses automatic grouping without category labels.
- Nodes or bands are crowded: Increase Y Spacing, choose Fan-out Curves, or select Center Screen after changing the layout.
- Connections are difficult to follow: Compare the available Line Style options or temporarily select one link list at a time.
- A dragged node will not move left or right: This is expected. The selected date controls its horizontal position.
- Nodes without a valid value in the selected date field cannot be placed and are omitted from the view.
- Dense networks can still contain overlapping paths; spacing and line-style controls reduce but may not eliminate every overlap.
- The view displays supplied relationships and dates but does not infer direction, exposure, or causality.
- Only links from the currently selected link lists are displayed.