Networks

Source: R/geom-net.r, R/stat-net.r

geom_net.Rd

The net geom is used visualize networks within the ggplot2 framework. geom_net combines the many parts of a network visualization into a single layer in ggplot2. It makes use of various other geoms, including but not limited to, geom_point , geom_segment , and geom_text .

geom_net(
 mapping = NULL,
 data = NULL,
 stat = "net",
 position = "identity",
 show.legend = NA,
 na.rm = FALSE,
 inherit.aes = TRUE,
 layout.alg = "kamadakawai",
 layout.par = list (),
 directed = FALSE,
 fiteach = FALSE,
 selfloops = FALSE,
 singletons = TRUE,
 alpha = 0.25,
 ecolour = NULL,
 ealpha = NULL,
 arrow = NULL,
 arrowgap = 0.01,
 arrowsize = 1,
 labelon = FALSE,
 labelcolour = NULL,
 labelgeom = "text",
 repel = FALSE,
 vertices = NULL,
 ...
)
GeomNet
StatNet
stat_net(
 mapping = NULL,
 data = NULL,
 geom = "net",
 position = "identity",
 show.legend = NA,
 inherit.aes = TRUE,
 layout.alg = "kamadakawai",
 layout.par = list (),
 fiteach = FALSE,
 vertices = NULL,
 singletons = TRUE,
 na.rm = FALSE,
 ...
)

Arguments

mapping	Set of aesthetic mappings created by `aes()` or `aes_()` . If specified and `inherit.aes = TRUE` (the default), it is combined with the default mapping at the top level of the plot. You must supply `mapping` if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If `NULL`, the default, the data is inherited from the plot data as specified in the call to `ggplot()` . A `data.frame`, or other object, will override the plot data. All objects will be fortified to produce a data frame. See `fortify()` for which variables will be created. A `function` will be called with a single argument, the plot data. The return value must be a `data.frame`, and will be used as the layer data. A `function` can be created from a `formula` (e.g. `~ head(.x, 10)`).
stat	The statistical transformation to use on the data for this layer, as a string.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
show.legend	logical. Should this layer be included in the legends? `NA`, the default, includes if any aesthetics are mapped. `FALSE` never includes, and `TRUE` always includes. It can also be a named logical vector to finely select the aesthetics to display.
na.rm	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
inherit.aes	If `FALSE`, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. `borders()` .
layout.alg	character. Value specifying the layout algorithm to use. Defaults to "kamadakawai". See `?sna::gplot.layout` documentation for more choices.
layout.par	list. Parameters detailing algorithmic specs. Default parameters from sna are used initially. See `?sna::gplot.layout` documentation for all options corresponding to all layouts.
directed	logical value. Should an arrow be drawn pointing to the `to_id` node? Default is `FALSE`.
fiteach	logical. Should the network be fit in each of the panels separately, or is there going to be one fit for all?
selfloops	logical value. Should loops (self-referencing edges) be shown (by drawing a circle adjacent to the corresponding node)? Default is `FALSE`.
singletons	logical. Should singletons (nodes with no incoming or outgoing ties) be plotted? Default is `TRUE`.
alpha	numeric. Value from 0-1 of alpha blending of nodes.
ecolour	character. Colour for edges.
ealpha	numeric. Value from 0-1 of alpha blending of edges.
arrow	what kind of arrow should be drawn? See `?grid::arrow` for more.
arrowgap	numeric value between 0 and 1 specifying how much (as a proportion of the line length) earlier the line segment should be stopped drawing before reaching the target node. This parameters is only regarded in directed networks.
arrowsize	numeric. How big should the arrow be drawn? Multiplicative of the default, 10 points.
labelon	logical. Include labels for all nodes. Labels are taken from the `from_id` variable, unless a `label` aesthetic is provided.
labelcolour	character. Colour for the labels. If this argument is not specified, labels have the same colour as the nodes.
labelgeom	character. Which ggplot2 `geom` should be used to draw the labels? Either `"text"` or `"label"`. Default is `"text"`
repel	logical. If `TRUE`, uses the ggrepel package geoms to draw the node labels instead of the ggplot2 geoms.
vertices	data frame. Dataset containing vertex information. Usage is a bit awkward, because every variable in this data set can only be used with the ggplot2 double dot representation ..varname.. Better: use the `fortify.edgedf` method
...	Other arguments passed on to `layer()` . These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `size = 3`. They may also be parameters to the paired geom/stat.
geom	`geom_net`, the geom attached to `stat_net` is called `"net"`.

Format

An object of class GeomNet (inherits from Geom, ggproto, gg) of length 6.

An object of class StatNet (inherits from Stat, ggproto, gg) of length 8.

Value

A data frame with additional columns:

x, y

coordinates of the nodes, beginning of edges,

xend, yend

coordinates end points of edges.

Aesthetics

geom_net understands the following aesthetics (required aesthetics are in bold):

from_id
to_id
x
y
alpha
colour
fontsize
group
label
linetype
linewidth
shape
size

Examples

if (FALSE) {
library (geomnet)
data (blood)
p <- ggplot(data = blood$edges, aes(from_id = from, to_id = to))
p + geom_net(vertices=blood$vertices, aes(colour=..type..)) + theme_net ()
bloodnet <- fortify(as.edgedf (blood$edges), blood$vertices)
p <- ggplot(data = bloodnet, aes(from_id = from_id, to_id = to_id))
p + geom_net()
p + geom_net(aes(colour=rho)) + theme_net ()
p + geom_net(aes(colour=rho), labelon=TRUE, vjust = -0.5)
p + geom_net(aes(colour=rho, linetype = group_to, label = from_id),
 vjust=-0.5, labelcolour="black", directed=TRUE) +
 theme_net ()
p + geom_net(colour = "orange", layout.alg = 'circle', size = 6)
p + geom_net(colour = "orange", layout.alg = 'circle', size = 6, linewidth=.75)
p + geom_net(colour = "orange", layout.alg = 'circle', size = 0, linewidth=.75,
 directed = TRUE)
p + geom_net(aes(size=Predominance, colour=rho, shape=rho, linetype=group_to),
 linewidth=0.75, labelon =TRUE, labelcolour="black") +
 facet_wrap(~Ethnicity) +
 scale_colour_brewer(palette="Set2")
gg <- ggplot(data = blood$edges, aes(from_id = from, to_id = to)) +
 geom_net(colour = "darkred", layout.alg = "circle", labelon=TRUE, size = 15,
 directed = TRUE, vjust = 0.5, labelcolour = "grey80",
 arrowsize = 1.5, linewidth = 0.5, arrowgap = 0.05,
 selfloops = TRUE, ecolour = "grey40") +
 theme_net ()
gg
dframe <- ggplot_build(gg)$data[[1]] # contains calculated node and edge values
#Madmen Relationships
data (madmen)
MMnet <- fortify(as.edgedf (madmen$edges), madmen$vertices)
p <- ggplot(data = MMnet, aes(from_id = from_id, to_id = to_id))
p + geom_net(labelon=TRUE)
p + geom_net(aes(colour=Gender), size=6, linewidth=1, labelon=TRUE, fontsize=3, labelcolour="black")
p + geom_net(aes(colour=Gender), size=6, linewidth=1, labelon=TRUE, labelcolour="black") +
 scale_colour_manual(values=c ("#FF69B4", "#0099ff")) + xlim (c (-.05,1.05))
p + geom_net(aes(colour=Gender), size=6, linewidth=1, directed=TRUE, labelon=TRUE,
 arrowgap=0.01, labelcolour="black") +
 scale_colour_manual(values=c ("#FF69B4", "#0099ff")) + xlim (c (-.05,1.05))
p <- ggplot(data = MMnet, aes(from_id = from_id, to_id = to_id))
# alternative labelling: specify label aesthetic.
p + geom_net(aes(colour=Gender, label=Gender), size=6, linewidth=1, fontsize=3,
 labelcolour="black")
## visualizing ggplot2 theme elements
data (theme_elements)
TEnet <- fortify(as.edgedf (theme_elements$edges[,c (2,1)]), theme_elements$vertices)
ggplot(data = TEnet, aes(from_id = from_id, to_id = to_id)) +
 geom_net(labelon=TRUE, vjust=-0.5)
## emails example from VastChallenge 2014
# care has to be taken to make sure that for each panel all nodes are included with
# the necessary information.
# Otherwise line segments show on the plot without nodes.
emailedges <- as.edgedf (subset (email$edges, nrecipients < 54))
emailnet <- fortify(emailedges, email$nodes)
#no facets
ggplot(data = emailnet, aes(from_id = from_id, to_id = to_id)) +
 geom_net(aes(colour= CurrentEmploymentType), linewidth=0.5) +
 scale_colour_brewer(palette="Set2")
#facet by day
emailnet <- fortify(emailedges, email$nodes, group = "day")
ggplot(data = emailnet, aes(from_id = from, to_id = to_id)) +
 geom_net(aes(colour= CurrentEmploymentType), linewidth=0.5, fiteach=TRUE) +
 scale_colour_brewer(palette="Set2") +
 facet_wrap(~day, nrow=2) + theme(legend.position="bottom")
ggplot(data = emailnet, aes(from_id = from, to_id = to_id)) +
 geom_net(aes(colour= CitizenshipCountry), linewidth=0.5, fiteach=TRUE) +
 scale_colour_brewer(palette="Set2") +
 facet_wrap(~day, nrow=2) + theme(legend.position="bottom")
ggplot(data = emailnet, aes(from_id = from, to_id = to_id)) +
 geom_net(aes(colour= CurrentEmploymentType), linewidth=0.5, fiteach=FALSE) +
 scale_colour_brewer(palette="Set2") +
 facet_wrap(~day, nrow=2) + theme(legend.position="bottom")
## Les Miserables example
data (lesmis)
lesmisnet <- fortify(as.edgedf (lesmis$edges), lesmis$vertices[, c (2,1)])
p <- ggplot(data=lesmisnet, aes(from_id=from_id, to_id=to_id))
p + geom_net(layout.alg="fruchtermanreingold")
p + geom_net(layout.alg="fruchtermanreingold", labelon=TRUE, vjust=-0.5)
p + geom_net(layout.alg="fruchtermanreingold", labelon=TRUE, vjust=-0.5,
 aes(linewidth=degree/5))
## College Football Games in the Fall 2000 regular season
# Source: http://www-/personal.umich.edu/~mejn/netdata/
data (football)
ftnet <- fortify(as.edgedf (football$edges), football$vertices)
p <- ggplot(data=ftnet, aes(from_id=from_id, to_id=to_id))
p + geom_net(aes(colour=value), linewidth=0.75, size=4.5, ecolour="grey80") +
 scale_colour_brewer("Conference", palette="Paired") + theme_net () +
 theme(legend.position="bottom")
 }