igraph (version 1.0.1)

shapes: 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.

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.

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.

Examples

# NOT RUN {
# 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))))
  str(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")
}
# }