Usage
xVisNet(g, pattern = NULL, colormap = c("yr", "jet", "gbr", "wyr",
"br",
"bwr", "rainbow", "wb"), ncolors = 40, zlim = NULL, colorbar = T,
newpage = T, signature = TRUE, glayout = layout_with_kk,
vertex.frame.color = NA, vertex.size = NULL, vertex.color = NULL,
vertex.shape = NULL, vertex.label = NULL, vertex.label.cex = NULL,
vertex.label.dist = 0.3, vertex.label.color = "blue",
edge.arrow.size = 0.3, ...)
Arguments
g
an object of class "igraph"
pattern
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)
colormap
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
http://html-color-codes.info/color-names ncolors
the number of colors specified over the colormap
zlim
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
colorbar
logical to indicate whether to append a colorbar. If
pattern is null, it always sets to false
newpage
logical to indicate whether to open a new page. By
default, it sets to true for opening a new page
signature
logical to indicate whether the signature is assigned
to the plot caption. By default, it sets FALSE
glayout
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_nicely" (previously "layout.auto"), "layout_randomly"
(previously "layout.random"), "layout_in_circle" (previously
"layout.circle"), "layout_on_sphere" (previously "layout.sphere"),
"layout_with_fr" (previously "layout.fruchterman.reingold"),
"layout_with_kk" (previously "layout.kamada.kawai"), "layout_as_tree"
(previously "layout.reingold.tilford"), "layout_with_lgl" (previously
"layout.lgl"), "layout_with_graphopt" (previously "layout.graphopt"),
"layout_with_sugiyama" (previously "layout.kamada.kawai"),
"layout_with_dh" (previously "layout.davidson.harel"),
"layout_with_drl" (previously "layout.drl"), "layout_with_gem"
(previously "layout.gem"), "layout_with_mds". A full explanation of
these layouts can be found in
http://igraph.org/r/doc/layout_nicely.html vertex.frame.color
the color of the frame of the vertices. If it
is NA, then there is no frame
vertex.size
the size of each vertex. If it is a vector, each
vertex may differ in size
vertex.color
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
ignored
vertex.shape
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". vertex.label
the label of the vertices. If it is NA, then there
is no label. The default vertex labels are the name attribute of the
nodes
vertex.label.cex
the font size of vertex labels.
vertex.label.dist
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.
vertex.label.color
the color of vertex labels.
edge.arrow.size
the size of the arrows for the directed edge.
The default value is 1.