R: Various vertex shapes when plotting igraph graphs

shapes {igraph} | R Documentation

## Various vertex shapes when plotting igraph graphs

### Description

Starting from version 0.5.1 igraph supports different vertex shapes when plotting graphs.

### Usage

    shapes(shape = NULL)

    shape_noclip(coords, el, params, end = c("both", "from", "to"))

    shape_noplot(coords, v = NULL, params)

    add_shape(shape, clip = shape_noclip, plot = shape_noplot,
      parameters = list())

### Arguments

`shape` | Character scalar, name of a vertex shape. If it is `NULL` for `shapes`, then the names of all defined vertex shapes are returned.
`coords, el, params, end, v` | See parameters of the clipping/plotting functions below.
`clip` | An R function object, the clipping function.
`plot` | An R function object, the plotting function.
`parameters` | Named list, additional plot/vertex/edge parameters. The element named define the new parameters, and the elements themselves define their default values. Vertex parameters should have a prefix ‘`vertex.`’, edge parameters a prefix ‘`edge.`’. Other general plotting parameters should have a prefix ‘`plot.`’. See Details below.

### Details

In igraph a vertex shape is defined by two functions: 1) provides information about the size of the shape for clipping the edges and 2) plots the shape if requested. These functions are called “shape functions” in the rest of this manual page. The first one is the clipping function and the second is the plotting function.

The clipping function has the following arguments:

coords

  A matrix with four columns, it contains the coordinates of the vertices for the edge list supplied in the `el` argument.

el

  A matrix with two columns, the edges of which some end points will be clipped. It should have the same number of rows as `coords`.

params

  This is a function object that can be called to query vertex/edge/plot graphical parameters. The first argument of the function is “`vertex`”, “`edge`” or “`plot`” to decide the type of the parameter, the second is a character string giving the name of the parameter. E.g.

      params("vertex", "size")

end

  Character string, it gives which end points will be used. Possible values are “`both`”, “`from`” and “`to`”. If “`from`” the function is expected to clip the first column in the `el` edge list, “`to`” selects the second column, “`both`” selects both.

The clipping function should return a matrix with the same number of rows as the `el` arguments. If `end` is `both` then the matrix must have four columns, otherwise two. The matrix contains the modified coordinates, with the clipping applied.

The plotting function has the following arguments:

coords

  The coordinates of the vertices, a matrix with two columns.

v

  The ids of the vertices to plot. It should match the number of rows in the `coords` argument.

params

  The same as for the clipping function, see above.

The return value of the plotting function is not used.

`shapes` can be used to list the names of all installed vertex shapes, by calling it without arguments, or setting the `shape` argument to `NULL`. If a shape name is given, then the clipping and plotting functions of that shape are returned in a named list.

`add_shape` can be used to add new vertex shapes to igraph. For this one must give the clipping and plotting functions of the new shape. It is also possible to list the plot/vertex/edge parameters, in the `parameters` argument, that the clipping and/or plotting functions can make use of. An example would be a generic regular polygon shape, which can have a parameter for the number of sides.

`shape_noclip` is a very simple clipping function that the user can use in their own shape definitions. It does no clipping, the edges will be drawn exactly until the listed vertex position coordinates.

`shape_noplot` is a very simple (and probably not very useful) plotting function, that does not plot anything.

### Value

`shapes` returns a character vector if the `shape` argument is `NULL`. It returns a named list with entries named ‘clip’ and ‘plot’, both of them R functions.

`add_shape` returns `TRUE`, invisibly.

`shape_noclip` returns the appropriate columns of its `coords` argument.

### Examples

    # all vertex shapes, minus "raster", that might not be available
    shapes <- setdiff(shapes(), "")
    g <- make_ring(length(shapes))
    set.seed(42)
    plot(g, vertex.shape=shapes, vertex.label=shapes, vertex.label.dist=1,
         vertex.size=15, vertex.size2=15,
         vertex.pie=lapply(shapes, function(x) if (x=="pie") 2:6 else 0),
         vertex.pie.color=list(heat.colors(5)))

    # add new vertex shape, plot nothing with no clipping
    add_shape("nil")
    plot(g, vertex.shape="nil")

    #################################################################
    # triangle vertex shape
    mytriangle <- function(coords, v=NULL, params) {
      vertex.color <- params("vertex", "color")
      if (length(vertex.color) != 1 && !is.null(v)) {
        vertex.color <- vertex.color[v]
      }
      vertex.size <- 1/200 * params("vertex", "size")
      if (length(vertex.size) != 1 && !is.null(v)) {
        vertex.size <- vertex.size[v]
      }

      symbols(x=coords[,1], y=coords[,2], bg=vertex.color,
              stars=cbind(vertex.size, vertex.size, vertex.size),
              add=TRUE, inches=FALSE)
    }
    # clips as a circle
    add_shape("triangle", clip=shapes("circle")$clip,
                     plot=mytriangle)
    plot(g, vertex.shape="triangle", vertex.color=rainbow(vcount(g)),
         vertex.size=seq(10,20,length=vcount(g)))

    #################################################################
    # generic star vertex shape, with a parameter for number of rays
    mystar <- function(coords, v=NULL, params) {
      vertex.color <- params("vertex", "color")
      if (length(vertex.color) != 1 && !is.null(v)) {
        vertex.color <- vertex.color[v]
      }
      vertex.size  <- 1/200 * params("vertex", "size")
      if (length(vertex.size) != 1 && !is.null(v)) {
        vertex.size <- vertex.size[v]
      }
      norays <- params("vertex", "norays")
      if (length(norays) != 1 && !is.null(v)) {
        norays <- norays[v]
      }

      mapply(coords[,1], coords[,2], vertex.color, vertex.size, norays,
             FUN=function(x, y, bg, size, nor) {
               symbols(x=x, y=y, bg=bg,
                       stars=matrix(c(size,size/2), nrow=1, ncol=nor*2),
                       add=TRUE, inches=FALSE)
             })
    }
    # no clipping, edges will be below the vertices anyway
    add_shape("star", clip=shape_noclip,
                     plot=mystar, parameters=list(vertex.norays=5))
    plot(g, vertex.shape="star", vertex.color=rainbow(vcount(g)),
         vertex.size=seq(10,20,length=vcount(g)))
    plot(g, vertex.shape="star", vertex.color=rainbow(vcount(g)),
         vertex.size=seq(10,20,length=vcount(g)),
         vertex.norays=rep(4:8, length=vcount(g)))

    #################################################################
    # Pictures as vertices.
    # Similar musicians from last.fm, we start from an artist and
    # will query two levels. We will use the XML, png and jpeg packages
    # for this, so these must be available. Otherwise the example is
    # skipped

    loadIfYouCan <- function(pkg) suppressWarnings(do.call(require, list(pkg)))

    if (loadIfYouCan("XML") && loadIfYouCan("png") &&
        loadIfYouCan("jpeg")) {
      url <- paste(sep="",
                   'http://ws.audioscrobbler.com/',
                   '2.0/?method=artist.getinfo&artist=%s',
                   '&api_key=1784468ada3f544faf9172ee8b99fca3')
      getartist <- function(artist) {
        cat("Downloading from last.fm. ... ")
        txt <- readLines(sprintf(url, URLencode(artist)))
        xml <- xmlTreeParse(txt, useInternal=TRUE)
        img <- xpathSApply(xml, "/lfm/artist/image[@size='medium'][1]",
                           xmlValue)
        if (img != "") {
          con <- url(img, open="rb")
          bin <- readBin(con, what="raw", n=10^6)
          close(con)
          if (grepl("\\\\.png$", img)) {
            rast <- readPNG(bin, native=TRUE)
          } else if (grepl("\\\\.jpe?g$", img)) {
            rast <- readJPEG(bin, native=TRUE)
          } else {
            rast <- as.raster(matrix())
          }
        } else {
          rast <- as.raster(numeric())
        }
        sim <- xpathSApply(xml, "/lfm/artist/similar/artist/name", xmlValue)
        cat("done.\\n")
        list(name=artist, image=rast, similar=sim)
      }

      ego <- getartist("Placebo")
      similar <- lapply(ego$similar, getartist)

      edges1 <- cbind(ego$name, ego$similar)
      edges2 <- lapply(similar, function(x) cbind(x$name, x$similar))
      edges3 <- rbind(edges1, do.call(rbind, edges2))
      edges <- edges3[ edges3[,1] %in% c(ego$name, ego$similar) &
                       edges3[,2] %in% c(ego$name, ego$similar), ]

      musnet <- simplify(graph_from_data_frame(edges, dir=FALSE,
                         vertices=data.frame(name=c(ego$name, ego$similar))))
      print_all(musnet)

      V(musnet)$raster <- c(list(ego$image), lapply(similar, "[[", "image"))
      plot(musnet, layout=layout_as_star, vertex.shape="raster",
           vertex.label=V(musnet)$name, margin=.2,
           vertex.size=50, vertex.size2=50,
           vertex.label.dist=2, vertex.label.degree=0)
    } else {
      message("You need the `XML', `png' and `jpeg' packages to run this")
    }

[Package igraph version 1.2.4.1 Index]