pathvisio-book/interactions.Rmd at main · PathVisio/pathvisio-book · GitHub

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# Interactions

An interaction represents the biological relation between entities.

An Xref can be specified for Interactions (in contrast to GraphicalLines).

```{r fig.align="center", echo=FALSE, out.width="70%", fig.cap = "Object Panel options for Interactions"}
knitr::include_graphics("images/screenshots/interactions.png")
```

## Basic interactions

### Directed      ![](images/figures/lines/directed.png){width=100}

### Undirected      ![](images/figures/lines/undirected.png){width=100}

## Interactions (Recommended)

### Conversion      ![](images/figures/lines/conversion.png){width=100}
mim-conversion; mim-modification; mim-cleavage; mim-gap; mim-branching-left; mim-branching-right

### Inhibition      ![](images/figures/lines/inhibition.png){width=100}
TBar	mim-inhibition

### Catalysis      ![](images/figures/lines/catalysis.png){width=100}
mim-catalysis

### Stimulation      ![](images/figures/lines/stimulation.png){width=100}
mim-stimulation; mim-necessary-stimulation

### Binding      ![](images/figures/lines/binding.png){width=100}
mim-binding; mim-covalent-bond

### Translocation      ![](images/figures/lines/translocation.png){width=100}
mim-translocation

### Transcription-translation      ![](images/figures/lines/transcription-translation.png){width=100}
mim-transcription-translation


## Adding an Anchor
An anchor is a connection point on a graphical line or an interaction, where another graphical line or interaction can be connected.

To add an anchor:

1. Right-click on the line > Add Anchor

![](images/gifs/add_anchor.gif){width=100%}


## Changing ConnectorType
The connector type specifies a set of rules to govern layout of lines, e.g. Straight (default), Elbow...

To change connector type:

1. Right-click on the Line > Connector Type > select a new type
2. Or select the Line, go to Properties Panel and change Connector Type using drop down menu

![](images/gifs/change_connectortype.gif){width=100%}


## Adding Waypoints (ConnectorType = "Segmented")
Waypoints can be added to a graphical line or an interaction of Segmente ConnectorType.

To add waypoints:

1. Line must have Connector type "Segmented"
2. Right-click on the Line > Add Waypoint

![](images/gifs/add_waypoint.gif){width=100%}