Author: Ursula Laa

# Edges in scatterplot displays

#### Ursula Laa

    library(tourr)

Showing connections between points can be useful in different applications, including geometric shapes, indicating patterns in sequential series or showing connections suggested by a model (for example in clustering). These edges can be added in the 2D scatterplot display (`display_xy`) through the `edges` argument, and should be specified as a two column integer matrix of the indices of ends of lines.

For example, we can generate cube vertices and edges using the `geozoo` package. The information stored as `points` constitutes the input data, and `edges` can directly be passed into the display.

    # generate 3D cube vertices
    cube <- geozoo::cube.iterate(3)
    # data is stored points, edges contains the needed two column matrix for connecting points
    cube$points
    cube$edges
    # call grand tour with the scatterplot (xy) display, turning off axes
    animate_xy(cube$points, edges = cube$edges, axes = "off")

Edges added to the vertices of a 3D cube.

We can use the same functions for higher dimensional cubes as well (but would not print the data).

    cube5 <- geozoo::cube.iterate(5)
    animate_xy(cube5$points, edges = cube5$edges, axes = "off")

Edges added to the vertices of a 5D cube.

It can often be useful to connect points with edges, for example sequential points in a time series, or points that are connected by a model. As a simple example we can connect centroids found when clustering the flea dataset:

    # get centroids of 3 clusters of the flea data
    n <- nrow(flea)
    set.seed(1019)
    flea_centroids <- stats::kmeans(flea[,1:6], 3)$centers
    flea_aug <- rbind(flea[,1:6], flea_centroids)
    col <- c(rep("black", n), rep("orange", 3))
    flea_edges <- matrix(c(n+1, n+2, n+1, n+3, n+2, n+3), ncol=2, byrow = TRUE)
    animate_xy(flea_aug, edges = flea_edges,
               col = col, edges.col = "orange",
               edges.width = 3)

Connecting the k-centroids with edges.