Vertex shapes

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Various vertex shapes when plotting igraph graphs

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

Keywords
graphs
Usage
vertex.shapes (shape = NULL)
add.vertex.shape (shape, clip = igraph.shape.noclip,
       plot = igraph.shape.noplot, parameters = list())
igraph.shape.noclip (coords, el, params, end = c("both", "from", "to"))
igraph.shape.noplot (coords, v = NULL, params)
Arguments
shape
Character scalar, name of a vertex shape. If it is NULL for vertex.shapes, then the names of all defined vertex shapes are returned.
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 pa
coords,el,params,end,v
See parameters of the clipping/plotting functions 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: [object Object],[object Object],[object Object],[object Object]

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: [object Object],[object Object],[object Object]

The return value of the plotting function is not used.

vertex.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.vertex.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.

igraph.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.

igraph.shape.noplot is a very simple (and probably not very useful) plotting function, that does not plot anything.

Value

  • vertex.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.vertex.shape returns TRUE, invisibly.

    igraph.shape.noclip returns the appropriate columns of its coords argument.

    igraph.shape.noplot returns NULL, invisibly.

concept

  • Vertex shapes
  • Visualization

See Also

igraph.plotting, plot.igraph

Aliases
  • igraph.vertex.shapes
  • vertex.shapes
  • add.vertex.shape
  • igraph.shape.noclip
  • igraph.shape.noplot
Examples
#################################################################
# all vertex shapes, minus "raster", that might not be available
shapes <- setdiff(vertex.shapes(), "")
g <- graph.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.vertex.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.vertex.shape("triangle", clip=vertex.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.vertex.shape("star", clip=igraph.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.data.frame(edges, dir=FALSE,
                     vertices=data.frame(name=c(ego$name, ego$similar))))
  str(musnet)
  
  V(musnet)$raster <- c(list(ego$image), lapply(similar, "[[", "image"))
  plot(musnet, layout=layout.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")
}
Documentation reproduced from package igraph, version 0.7.1, License: GPL (>= 2)

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