R: Interactive 3D Graph Visualization

graphjs {threejs} | R Documentation

## Interactive 3D Graph Visualization

### Description

Make interactive 3D plots of `igraph` objects.

### Usage

    graphjs(g, layout, vertex.color, vertex.size, vertex.shape, vertex.label,
      edge.color, edge.width, edge.alpha, main = "", bg = "white",
      width = NULL, height = NULL, ...)

### Arguments

`g` | an `igraph` graph object or a list of `igraph` objects (see notes)
`layout` | optional graph layout or list of layouts (see notes)
`vertex.color` | optional vertex color or vector of colors as long as the number of vertices in `g`
`vertex.size` | optional vertex size or vector of sizes
`vertex.shape` | optional vertex shape or vector of shapes
`vertex.label` | optional mouse-over vertex label or vector of labels
`edge.color` | optional edge color or vector of colors as long as the number of edges in `g`
`edge.width` | optional edge width (single scalar value, see notes)
`edge.alpha` | optional single numeric edge transparency value
`main` | plot title text
`bg` | plot background color
`width` | the widget container `div` width in pixels
`height` | the widget container `div` height in pixels
`...` | optional additional arguments passed to `scatterplot3js`

### Value

An htmlwidget object that is displayed using the object's show or print method. (If you don't see your widget plot, try printing it with the `print` function.)

### Interacting with the plot

Press and hold the left mouse button, or touch or trackpad equivalent, and move the mouse to rotate the plot. Press and hold the right mouse button to pan. Use the mouse scroll wheel to zoom. If `vertex.label`s are specified (see below), moving the mouse pointer over a point will display the label. Altenatively use `vertex.shape` to plot character names as shown in the examples below. Set the optional experimental `use.orbitcontrols=TRUE` argument to use a more CPU-efficient but somewhat less fluid mouse/touch interface.

### Layout options

Use the `layout` parameter to control the visualization layout by supplying either a three-column matrix of vertex `x, y, z` coordinates, or a function that returns such a layout. The igraph `layout_with_fr` force-directed layout is used by default (note that only 3D layouts are supported). Also see the animation section below.

### Vertex options

Optional parameters beginning with `vertex.` represent a subset of the igraph package vertex visualization options and work similarly, see `link{igraph.plotting}`. Vertex shapes in `graphjs` act somewhat differently, and are mapped to the `pch` option in `scatterplot3js`. In particular, `pch` character symbols or even short text strings may be specified. The `vertex.label` option enables a mouse-over label display instead of plotting lables directly near the vertices. (Consider using the text `pch` options for that instead.)

### Edge options

Optional parameters beginning with `edge.` represent a subset of the igraph edge visualization options and work similarly as the `vertex.` options above. The current version of the package only supports uniform edge widths specified by a single scalar value. This choice was made for performance reasons to support large visualizations.

### Graph animation

Specifying a list of three-column layout matrices in `layout` displays a linear interpolation from one layout to the next, providing a simple mechanism for graph animation. Each layout must have the same number of rows as the number of vertices in the graph.

Specify the optional `fpl` (frames per layout) parameter to control the number of interpolating animation frames between layouts. See the examples.

Optionally specify a list of graph objects in `g` to vary the displayed edges and edge colors from one layout to the next, with the restriction that each graph object must refer to a uniform number of vertices.

The lists of graphs may optionally include varying vertex and edge colors. Alternatively, specify a list of `vertex.color` vectors (one for each layout) to animate vertex colors. Similarly, optionally specify a list of `edge.color` vectors to animate edge colors.

Optionally provide a list of `main` title text strings to vary the title with each animation layout.

None of the other plot parameters may be animated.

### Click animation

Specify the option `click=list` to animate the graph when specified vertices are clicked interactively, where `list` is a named list of animation entries. Each entry must itself be a list with the following entries

- g optional a single igraph object with the same number of vertices as `g` above (if specified this must be the first entry)

- layout - optional a single igraph layout, or differential layout if `cumulative=TRUE`

- vertex.color - optional single vector of vertex colors

- edge.color - optional single vector of edge colors

- cumulative - optional boolean entry, if `TRUE` then vertex positions are added to current plot, default is `FALSE`

At least one of `g` or `layout` must be specified in each animation list entry. The layouts and colors may be alternatively imbedded in the igraph object itself. Each animation list entry must be named by a number corresponding to the vertex enumeration in `g`. An animation sequence is triggered when a corresponding vertex is clicked. For instance, to trigger animations when vertices number 1 or 5 are clicked, include list entries labeled `"1"` and `"5"`. See the demos in `demo(package="threejs")` for detailed examples.

### Other interactions

Specify the argument `brush=TRUE` to highlight a clicked vertex and its directly connected edges (click off of a vertex to reset the display). Optionally set the `highlight=<hex color>` and `lowlight=<hex color>` to manually control the brushing display colors.

### Crosstalk

`graphjs()` works with crosstalk selection (but not filtering yet); see https://rstudio.github.io/crosstalk/. Enable crosstalk by supplying the optional agrument `crosstalk=df`, where `df` is a crosstalk-SharedData data.frame-like object with the same number of rows as graph vertices (see the examples).

### Note

Edge transparency values specified as part of `edge.color` are ignored, however you can set an overall transparency for edges with `edge.alpha`.

### References

The three.js project http://threejs.org.

### See Also

`igraph.plotting`, `scatterplot3js`

### Examples

    set.seed(1)
    g <- sample_islands(3, 10, 5/10, 1)
    i <- cluster_optimal(g)
    (graphjs(g, vertex.color=c("orange", "green", "blue")[i$membership], vertex.shape="sphere"))

    # Les Miserables Character Co-appearance Data
    data("LeMis")
    (graphjs(LeMis))

    # ...plot Character names
    (graphjs(LeMis, vertex.shape=V(LeMis)$label))

    # SNAP Facebook ego network dataset
    data("ego")
    (graphjs(ego, bg="black"))

    ## Not run:
    # A shiny example
    shiny::runApp(system.file("examples/graph", package="threejs"))

    # A graph amination that shows several layouts
    data("LeMis")
    graphjs(LeMis,
      layout=list(
        layout_randomly(LeMis, dim=3),
        layout_on_sphere(LeMis),
        layout_with_drl(LeMis, dim=3),  # note! somewhat slow...
        layout_with_fr(LeMis, dim=3, niter=30)),
      main=list("random layout", "sphere layout", "drl layout", "fr layout"),
      fpl=300)

    # A simple graph animation illustrating edge modification
    g <- make_ring(5) - edges(1:5)
    graph_list <- list(
     g + edge(1, 2),
     g + edge(1, 2) + edge(2, 3),
     g + edge(1, 2) + edge(2, 3) + edge(3, 4),
     g + edge(1, 2) + edge(2, 3) + edge(3, 4) + edge(4, 5),
     g + edge(1, 2) + edge(2, 3) + edge(3, 4) + edge(4, 5) + edge(5, 1))
     graphjs(graph_list, main=paste(1:5),
       vertex.color=rainbow(5), vertex.shape="sphere", edge.width=3)

    # see `demo(package="threejs") for more animation demos.

    # A crosstalk example
    library(crosstalk)
    library(DT)
    data(LeMis)
    sd = SharedData$new(data.frame(Name = V(LeMis)$label))
    print(bscols(
      graphjs(LeMis, brush=TRUE, crosstalk=sd),
      datatable(sd, rownames=FALSE, options=list(dom='tp'))
    ))

    ## End(Not run)

[Package threejs version 0.3.1 Index]