-
Notifications
You must be signed in to change notification settings - Fork 15
/
util-plot.R
242 lines (212 loc) · 11.6 KB
/
util-plot.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
## This file is part of coronet, which is free software: you
## can redistribute it and/or modify it under the terms of the GNU General
## Public License as published by the Free Software Foundation, version 2.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License along
## with this program; if not, write to the Free Software Foundation, Inc.,
## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
##
## Copyright 2017-2018, 2020 by Claus Hunsen <hunsen@fim.uni-passau.de>
## Copyright 2018 by Barbara Eckl <ecklbarb@fim.uni-passau.de>
## Copyright 2018 by Thomas Bock <bockthom@fim.uni-passau.de>
## Copyright 2020-2021 by Thomas Bock <bockthom@cs.uni-saarland.de>
## Copyright 2024 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
## All Rights Reserved.
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Libraries ---------------------------------------------------------------
requireNamespace("igraph") # networks
requireNamespace("ggplot2") ## plotting
requireNamespace("ggraph") ## plotting networks
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Global plot options -----------------------------------------------------
## (e.g., vertex size and colors)
## vertex-type names
PLOT.VERTEX.TYPE.AUTHOR = "Developer" # TYPE.AUTHOR
PLOT.VERTEX.TYPE.ARTIFACT = TYPE.ARTIFACT # "Artifact"
## vertex size
PLOT.VERTEX.SIZE = 10
PLOT.VERTEX.SIZE.LEGEND = PLOT.VERTEX.SIZE / 2
## vertex-label color
PLOT.VERTEX.LABEL.COLOR = "gray60"
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Plot functions ----------------------------------------------------------
#' Construct a ggplot2/ggraph plot object for the given network and print it directly.
#'
#' As a layout, by default, the "kk" layout from igraph (also known as "layout_kamada_kawai") is used,
#' is used, unless a graph attribute "layout" is set. For a comprehensive list of layouts and more information
#' on layouts in general, see \link{https://igraph.org/python/doc/tutorial/tutorial.html#layout-algorithms}.
#' To set the graph attribute on your network, run the following code while replacing \code{layout.to.set}
#' to your liking: \code{network = igraph::set.graph.attribute(network, "layout", layout.to.set)}.
#' Note that \code{layout.to.set} refers to one of the "short names" of the recpective igraph layout, as
#' specified on the Web site in the link given above.
#'
#' Note: The names for the vertex types are taken from the variables \code{PLOT.VERTEX.TYPE.AUTHOR} and
#' \code{PLOT.VERTEX.TYPE.ARTIFACT}. The defaults are \code{"Developer"} and \code{TYPE.ARTIFACT}, respectively.
#' All loops are deleted for plotting the network.
#'
#' @param network the network to plot and print
#' @param labels logical indicating whether vertex lables should be plotted [default: TRUE]
#'
#' @return the network (invisibly)
#'
#' @aliases plot.print.network
plot.network = function(network, labels = TRUE) {
plot.print.network(network, labels = labels)
}
#' Construct a ggplot2/ggraph plot object for the given network and print it directly.
#'
#' As a layout, by default, the "kk" layout from igraph (also known as "layout_kamada_kawai") is used,
#' is used, unless a graph attribute "layout" is set. For a comprehensive list of layouts and more information
#' on layouts in general, see \link{https://igraph.org/python/doc/tutorial/tutorial.html#layout-algorithms}.
#' To set the graph attribute on your network, run the following code while replacing \code{layout.to.set}
#' to your liking: \code{network = igraph::set.graph.attribute(network, "layout", layout.to.set)}.
#' Note that \code{layout.to.set} refers to one of the "short names" of the recpective igraph layout, as
#' specified on the Web site in the link given above.
#'
#' Note: The names for the vertex types are taken from the variables \code{PLOT.VERTEX.TYPE.AUTHOR} and
#' \code{PLOT.VERTEX.TYPE.ARTIFACT}. The defaults are \code{"Developer"} and \code{TYPE.ARTIFACT}, respectively.
#' All loops are deleted for plotting the network.
#'
#' @param network the network to plot and print
#' @param labels logical indicating whether vertex lables should be plotted [default: TRUE]
#'
#' @return the network (invisibly)
#'
#' @aliases plot.network
plot.print.network = function(network, labels = TRUE) {
p = plot.get.plot.for.network(network, labels = labels)
print(p)
}
#' Construct a ggplot2/ggraph plot object for the given network.
#'
#' As a layout, by default, the "kk" layout from igraph (also known as "layout_kamada_kawai") is used,
#' is used, unless a graph attribute "layout" is set. For a comprehensive list of layouts and more information
#' on layouts in general, see \link{https://igraph.org/python/doc/tutorial/tutorial.html#layout-algorithms}.
#' To set the graph attribute on your network, run the following code while replacing \code{layout.to.set}
#' to your liking: \code{network = igraph::set.graph.attribute(network, "layout", layout.to.set)}.
#' Note that \code{layout.to.set} refers to one of the "short names" of the recpective igraph layout, as
#' specified on the Web site in the link given above.
#'
#' Note: The names for the vertex types are taken from the variables \code{PLOT.VERTEX.TYPE.AUTHOR} and
#' \code{PLOT.VERTEX.TYPE.ARTIFACT}. The defaults are \code{"Developer"} and \code{TYPE.ARTIFACT}, respectively.
#' All loops are deleted for plotting the network.
#'
#' @param network the network to plot
#' @param labels logical indicating whether vertex lables should be plotted [default: TRUE]
#'
#' @return a ggplot2/ggraph plot object
plot.get.plot.for.network = function(network, labels = TRUE) {
## check if network is empty
if (igraph::vcount(network) == 0) {
network = create.empty.network(directed = igraph::is.directed(network), add.attributes = TRUE)
PLOT.VERTEX.SIZE = 0
}
## properly set vertex-type names for legend
PLOT.VERTEX.TYPES = c(PLOT.VERTEX.TYPE.AUTHOR, PLOT.VERTEX.TYPE.ARTIFACT)
names(PLOT.VERTEX.TYPES) = c(TYPE.AUTHOR, TYPE.ARTIFACT)
## remove loops because of weird behavior when plotting
network = igraph::delete.edges(network, igraph::E(network)[igraph::is.loop(network)])
## fix the type attributes (add new ones, also named)
network = plot.fix.type.attributes(network)
## set igraph network layout if no layout is set yet
if (!("layout" %in% igraph::list.graph.attributes(network))) {
network = igraph::set.graph.attribute(network, "layout", "kk")
}
layout.algorithm = igraph::get.graph.attribute(network, "layout")
## create a ggraph object using the specified igraph layout
p = ggraph::ggraph(network, layout = layout.algorithm)
## plot edges if there are any
if (igraph::ecount(network) > 0) {
p = p +
ggraph::geom_edge_fan(
mapping = ggplot2::aes(colour = paste(relation, sep = " "), linetype = edge.type, width = 0.3 + 0.5 * log(weight)),
end_cap = ggraph::circle(PLOT.VERTEX.SIZE + 3, "pt"),
start_cap = ggraph::circle(PLOT.VERTEX.SIZE + 3, "pt"),
arrow = if (igraph::is.directed(network)) {
ggplot2::arrow(length = ggplot2::unit(PLOT.VERTEX.SIZE / 2, 'pt'), ends = "last", type = "closed")
} else {
NULL
}
)
}
## construct plot with proper colors and shapes everywhere
p = p +
## plot vertices
ggraph::geom_node_point(ggplot2::aes(color = kind, shape = vertex.type), size = PLOT.VERTEX.SIZE) +
ggraph::geom_node_text(ggplot2::aes(label = if (labels) name else c("")), size = 3.5, color = PLOT.VERTEX.LABEL.COLOR) +
## scale vertices (colors and styles)
ggplot2::scale_shape_discrete(name = "Vertex Types", solid = TRUE) +
viridis::scale_color_viridis(name = "Vertices", option = "plasma", discrete = TRUE,
end = 0.8, begin = 0.05) +
## scale edges (colors and styles)
ggraph::scale_edge_linetype(name = "Relation Types") +
ggplot2::discrete_scale(name = "Relations", "edge_colour", "viridis",
viridis::viridis_pal(option = "viridis", end = 0.8, begin = 0.25)) +
## BROKEN RIGHT NOW due to bug in scale_edge_colour_viridis():
# ggraph::scale_edge_colour_viridis(name = "Relations", option = "magma", discrete = TRUE,
# end = 0.85, begin = 0, direction = 1) +
## theme
ggplot2::theme_light() +
ggplot2::guides(
## reduce size of symbols in legend
shape = ggplot2::guide_legend(override.aes = list(size = PLOT.VERTEX.SIZE.LEGEND)),
color = ggplot2::guide_legend(override.aes = list(size = PLOT.VERTEX.SIZE.LEGEND, shape = 15))
) +
ggplot2::theme(
legend.position = "bottom",
legend.box = "horizontal", # orientation for complete legend
legend.direction = "vertical", # orientation for each sublegend/guide
axis.line = ggplot2::element_blank(),
axis.text.x = ggplot2::element_blank(),
axis.text.y = ggplot2::element_blank(),
axis.ticks = ggplot2::element_blank(),
axis.title.x = ggplot2::element_blank(),
axis.title.y = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
panel.grid.major = ggplot2::element_blank(),
panel.grid.minor = ggplot2::element_blank(),
plot.background = ggplot2::element_blank()
)
return(p)
}
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Low-level functionality -------------------------------------------------
#' Extend and transform the 'type' attribute of vertices and edges in the given network to get
#' more flexibility while plotting.
#'
#' Note: By default, the 'type' attribute of vertices is set either to 'TYPE.AUTHOR' or 'TYPE.ARTIFACT',
#' the 'type' attribute of edges is set to 'TYPE.EDGES.INTER' or 'TYPE.EDGES.INTRA'.
#'
#' This function transforms the vertex attribute 'type' to logical values for better plotting with the
#' plot layout 'bipartite'. The mapping is as follows:
#' - TYPE.AUTHOR = FALSE, and
#' - TYPE.ARTIFACT = TRUE.
#'
#' Furthermore, the following attributes are added to either vertices or edges:
#' - vertex.type = a copy of the old vertex attribute 'type', and
#' - edge.type = a copy of the old edge attribute 'type'.
#'
#' @param network the igraph object to augment
#'
#' @return the old network with the new and changed vertex and edge attributes
plot.fix.type.attributes = function(network) {
## copy type attribute to vertex.type and edge.type
if (igraph::vcount(network) == 0) {
network = igraph::set.vertex.attribute(network, "vertex.type", value = NA)
} else {
network = igraph::set.vertex.attribute(network, "vertex.type", value = igraph::get.vertex.attribute(network, "type"))
}
network = igraph::set.edge.attribute(network, "edge.type", value = igraph::get.edge.attribute(network, "type"))
## adjust 'type' attribute for vertices for bipartite plotting (we need Booleans there)
types = igraph::get.vertex.attribute(network, "type")
network = igraph::remove.vertex.attribute(network, "type")
network = igraph::set.vertex.attribute(network, "type", value = sapply(
types, function(t) return(t == TYPE.ARTIFACT)
))
return(network)
}