visNet is supposed to visualise a graph object of class "igraph"
or "graphNEL". It also allows the color-coding of vertices by providing
the input pattern.
visNet(g, pattern = NULL, colormap = c("bwr", "jet", "gbr", "wyr", "br", "yr", "rainbow",
"wb"), ncolors = 40, zlim = NULL, colorbar = T, newpage = T, glayout = layout.fruchterman.reingold,
vertex.frame.color = NA, vertex.size = NULL, vertex.color = NULL, vertex.shape = NULL,
vertex.label = NULL, vertex.label.cex = NULL, vertex.label.dist = NULL, vertex.label.color = "black",
- an object of class "igraph" or "graphNEL"
- a numeric vector used to color-code vertices/nodes.
Notably, if the input vector contains names, then these names should
include all node names of input graph, i.e. V(g)$name, since there is a
mapping operation. After mapping, the length of the patern vector
should be the same as the number of nodes of input graph; otherwise,
this input pattern will be ignored. The way of how to color-code is to
map values in the pattern onto the whole colormap (see the next
arguments: colormap, ncolors, zlim and colorbar)
- short name for the colormap. It can be one of "jet"
(jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red
colormap), "wyr" (white-yellow-red colormap), "br" (black-red
colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and
"rainbow" (rainbow colormap, that is,
red-yellow-green-cyan-blue-magenta). Alternatively, any
hyphen-separated HTML color names, e.g. "blue-black-yellow",
"royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of
standard color names can be found in
- the number of colors specified over the colormap
- the minimum and maximum z/patttern values for which colors
should be plotted, defaulting to the range of the finite values of z.
Each of the given colors will be used to color an equispaced interval
of this range. The midpoints of the intervals cover the range, so that
values just outside the range will be plotted
- logical to indicate whether to append a colorbar. If
pattern is null, it always sets to false
- logical to indicate whether to open a new page. By
default, it sets to true for opening a new page
- either a function or a numeric matrix configuring how
the vertices will be placed on the plot. If layout is a function, this
function will be called with the graph as the single parameter to
determine the actual coordinates. This function can be one of
"layout.auto", "layout.random", "layout.circle", "layout.sphere",
"layout.fruchterman.reingold", "layout.kamada.kawai", "layout.spring",
"layout.lgl", "layout.graphopt", "layout.svd" and "layout.norm". A full
explanation of these layouts can be found in
- the color of the frame of the vertices. If it
is NA, then there is no frame
- the size of each vertex. If it is a vector, each
vertex may differ in size
- the fill color of the vertices. If it is NA, then
there is no fill color. If the pattern is given, this setup will be
- the shape of each vertex. It can be one of
"circle", "square", "csquare", "rectangle", "crectangle", "vrectangle",
"pie" (http://igraph.org/r/doc/vertex.shape.pie.html), "sphere",
and "none". If it sets to NULL, these vertices with negative will be
"csquare" and the rest "circle".
- the label of the vertices. If it is NA, then there
is no label. The default vertex labels are the name attribute of the
- the font size of vertex labels.
- the distance of the label from the center of
the vertex. If it is 0 then the label is centered on the vertex. If it
is 1 then the label is displayed beside the vertex.
- the color of vertex labels.
- additional graphic parameters. See
http://igraph.org/r/doc/plot.common.html for the complete list.
# 1) generate a random graph according to the ER model
g <- erdos.renyi.game(100, 1/100)
# 2) produce the induced subgraph only based on the nodes in query
subg <- dNetInduce(g, V(g), knn=0)
# 3) visualise the subg with vertices being color-coded by the pattern
pattern <- runif(vcount(subg))
names(pattern) <- V(subg)$name
visNet(g=subg, pattern=pattern, colormap="bwr", vertex.shape="sphere")