Rescale vertex size to be used in plot.igraph. — rescale_vertex

This function rescales a vertex size before passing it to plot.igraph so that the resulting vertices have the desired size relative to the x-axis.

rescale_vertex_igraph(
  vertex.size,
  par.usr = par("usr"),
  minmax.relative.size = getOption("diffnet.minmax.relative.size", c(0.01, 0.04)),
  adjust = 200
)

igraph_vertex_rescale(
  vertex.size,
  par.usr = par("usr"),
  minmax.relative.size = getOption("diffnet.minmax.relative.size", c(0.01, 0.04)),
  adjust = 200
)

vertex_rescale_igraph(
  vertex.size,
  par.usr = par("usr"),
  minmax.relative.size = getOption("diffnet.minmax.relative.size", c(0.01, 0.04)),
  adjust = 200
)

Arguments

vertex.size: Numeric vector of unscaled vertices' sizes. This is unit-free.
par.usr: Integer vector of length 4 with the coordinates of plotting region. by default uses par("usr").
minmax.relative.size: A numeric vector of length 2. Represents the desired min and max vertex sizes relative to the x-axis in terms of percentage (see details).
adjust: Numeric scalar. Adjustment made to the resulting adjusted size (see details).

Value

An integer vector of the same length as vertex.size with rescaled values.

Details

minmax.relative.size limits the minimum and maximum size that a vertex can take in the plot relative to the x-axis scale. The values for the x-axis scale are by default retrieved by accessing to par("usr"). By default the vertex are rescaled to be at least 1% of the size of the plotting region and no more than 5% of the plotting region, minmax.relative.size=c(.01, .05).

The default value for adjust is taken from igraph version 1.0.1. In particular, the function igraph:::.igraph.shape.circle.plot, in which before passing the vertex.size to the function symbols, the vertex size is reduced by 200.

The rescaling is as follows: $$% v' = \frac{v - \underbar v}{\bar v - \underbar v}\times (\bar s - \underbar s) + \underbar s $$

Where $v$ is the vertex size, $\bar v$ and $\underbar v$ are the max and min values of $v$ respectively, and $\bar s$ and $\underbar s$ are the max and min size that vertices take in terms of minmax.relative.size and par.usr. The adjusted value $v'$ is then multiplied by adjust.

igraph_vertex_rescale and vertex_rescale_igraph are aliases.

Author

George G. Vega Yon

Examples


library(igraph)
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:ape’:
#> 
#>     degree, edges, mst, ring
#> The following objects are masked from ‘package:sna’:
#> 
#>     betweenness, bonpow, closeness, components, degree, dyad.census,
#>     evcent, hierarchy, is.connected, neighborhood, triad.census
#> The following objects are masked from ‘package:network’:
#> 
#>     %c%, %s%, add.edges, add.vertices, delete.edges, delete.vertices,
#>     get.edge.attribute, get.edges, get.vertex.attribute, is.bipartite,
#>     is.directed, list.edge.attributes, list.vertex.attributes,
#>     set.edge.attribute, set.vertex.attribute
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union

# Random graph and coordinates
set.seed(2134)
g <- barabasi.game(10)
#> Warning: `barabasi.game()` was deprecated in igraph 2.0.0.
#> ℹ Please use `sample_pa()` instead.
coords <- layout_nicely(g)

# Random size and figures
size <- runif(10)
size <- cbind(size, size)
shap <- sample(c("circle", "square"),10,TRUE)

# Plotting
oldpar <- par(no.readonly = TRUE)
par(mfrow=c(2,2), mai=rep(.5,4))
for (i in seq(1, 1000, length.out = 4)) {
  # New plot-window
  plot.new()
  plot.window(xlim=range(coords[,1]*i), ylim=range(coords[,2]*i))

  # plotting graph
  plot(g, layout=coords*i, add=TRUE, rescale=FALSE,
       vertex.shape = shap,
       vertex.size  = rescale_vertex_igraph(size) # HERE WE RESCALE!
  )

  # Adding some axis
  axis(1, lwd=0, lwd.ticks = 1)
  axis(2, lwd=0, lwd.ticks = 1)
  box()
}


par(oldpar)

Rescale vertex size to be used in `plot.igraph`.

Arguments

Value

Details

See also

Author

Examples