# ReadConnections

Auto-generated from the config schema in the source — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Provided by the `alignments` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/alignments/src/LinearAlignmentsDisplay/readConnectionsConfigSchema.ts).

The alignments display's `readConnections` setting: the band of
connections between mates and split segments, drawn as arcs or as the read
cloud, which plots each pair at its insert size. The connectors drawn over
the pileup's own rows are `pileup.showConnectors`, and which connections
either draws is the display's `filter.connections`.

## Example usage

```js
{
  type: 'LinearAlignmentsDisplay',
  readConnections: {
    show: true,
    mark: 'cloud',
    color: { field: 'insertSize' },
  },
}
```

```js
{
  type: 'LinearAlignmentsDisplay',
  readConnections: { show: true, showOrdinaryPairs: false },
  filter: { connections: { interchrom: 'only' } },
}
```

## Config slots

A setting written to it names members one by one: a member left out stays as it is, and `null` resets one. Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface.

| Slot | Description |
| --- | --- |
| **show**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>false</code> | draw the read connections |
| **mark**<br>[`stringEnum`](https://jbrowse.org/jb2/docs/config_guides/slot_types#stringenum) (arc, cloud) = <code>'arc'</code> | The two share one band and differ in shape, y scale and one cut: an arc rises with the span between its ends, and the cloud draws a flat line at \|TLEN\| on a log scale and leaves the pairs of modal insert size out unless `showOrdinaryPairs` keeps them. |
| **height**<br>[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#number) = <code>35</code> | height in pixels of the connections' own band, drawn under placement: 'down', or under 'up' while the coverage band is hidden; with coverage shown, up arcs draw in its height |
| **placement**<br>[`stringEnum`](https://jbrowse.org/jb2/docs/config_guides/slot_types#stringenum) (up, down) = <code>'down'</code> | where the connections draw: up over the coverage band, or down in a separate band below it |
| **lineWidth**<br>[`number`](https://jbrowse.org/jb2/docs/config_guides/slot_types#number) = <code>1</code> | width of each arc or line in pixels |
| **color**<br>[AlignmentsArcColor](../alignmentsarccolor) | The field that colors the connections; `""` uses the reads' `color` field where a connection paints it. |
| **showOrdinaryPairs**<br>[`maybeBoolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#the-maybe-types) | Unset, the mark decides: arcs draw ordinary pairs as context and the cloud leaves them out. |