Following ggraph v2.0 the tidygraph package
has been used as the central data structure. The integration goes beyond
using it as a simple background engine and has deep implications for
what you can do and how you can do it when plotting with
ggraph. This vignette will go into the details of the
ggraph/tidygraph relationship — buckle up…
Prior to v2 ggraph had two main supported data
structures, namely dendrogram and igraph. In
addition hclust and network were supported by
automatic conversion to dendrogram and igraph
respectively. Each of the two data structures had their own layouts and
under the hood two different set of functionality had to be maintained
to extract nodes and edges etc. In v2 and going forward this has been
simplified and ggraph now uses only tbl_graph
as a graph representation. This does not mean that you’re out of luck if
you’re not buying into the whole tidygraph idea. Every
object supported by tidygraph is supported directly in
ggraph by automatic conversion to tbl_graph.
This means that igraph, dendrogram,
hclust, and network is still supported in
addition to data.tree, phylo, and
graph as well as a number of data.frame,
matrix, and list representations.
The change has reduced internal code complexity quite a bit which
will make it easier to provide new features in future. From a user point
of view it has the benefit of simplifying the API in that
ggraph doesn’t really care what type of network object you
pass in - every layout and geom just works with every data structure.
Further, it simplifies how to add ggraph support to
additional data structures: just write an as_tbl_graph()
method for the class!. Due to the large support of classes and data
structures in tidygraph this should relatively
straightforward. If you’re developer of a package that defines a custom
network class simply export an as_tbl_graph() method for
the class to gain native ggraph (and
tidygraph) support, or add it directly to
tidygraph through a PR.
This simplification for both me and the users have really been the
motivation for the integration of tidygraph but as it were
it has also allowed or instigated a number of cool new features that
will be explored below.
In ggraph the initiation will need to specify a layout
to use for the subsequent node and edge geoms. Many of these layouts use
different node and edge variables in their calculations e.g. a node size
or an edge weight. Prior to v2 these arguments would simply take a
string naming the respective variable to use, but following the v2
update these arguments implement Non-Standard Evaluation (NSE) in a
manner known from both dplyr and ggplot2 where
it is used inside aes() calls. Depending on whether the
argument refers to a node or edge value the provided expression will be
evaluated in the context of nodes or edges respectively. The bottomline
is that given a network such as this:
library(tidygraph)
graph <- as_tbl_graph(
data.frame(
from = sample(5, 20, TRUE),
to = sample(5, 20, TRUE),
weight = runif(20)
)
)
graph## # A tbl_graph: 5 nodes and 20 edges
## #
## # A directed multigraph with 1 component
## #
## # Node Data: 5 × 1 (active)
## name
## <chr>
## 1 4
## 2 3
## 3 1
## 4 5
## 5 2
## #
## # Edge Data: 20 × 3
## from to weight
## <int> <int> <dbl>
## 1 1 2 0.207
## 2 2 1 0.594
## 3 2 2 0.859
## # … with 17 more rows
Then, instead of writing:
ggraph(graph, layout = 'fr', weights = "weight") +
geom_edge_link() +
geom_node_point()You would simply write:
ggraph(graph, layout = 'fr', weights = weight) +
geom_edge_link() +
geom_node_point()This change means that it is much easier to experiment with modifications to node and edge parameters affecting layouts as it is not necessary to modify the underlying graph but only the plotting code, e.g.:
ggraph(graph, layout = 'fr', weights = exp(weight)) +
geom_edge_link() +
geom_node_point()The most important improvement resulting from the integration of
tidygraph and ggraph is that
tidygraph algorithms are now directly usable within
ggraph calls. This means that it is no longer necessary to
precompute and store derived node and edge variables on the graph in
order to use them in a plot:
graph <- create_notable('zachary')
ggraph(graph, layout = 'fr') +
geom_edge_link() +
geom_node_point(aes(size = centrality_pagerank())) +
theme(legend.position = 'bottom')here it is not necessary to first compute the pagerank centrality and store it as a node variable in order to plot it, and if you’re interested in looking at one of the myriad of other centrality measures you simply change the plotting code. This feature makes it much easier and painfree to investigate the effect of different graph measures on your plots and is a huge benefit when iterating on your visualisation.
Access to tidygraph is available within
ggraph() and aes() calls, and within
facet formulas. It is thus possible to use algorithms when
specifying layouts, adding aesthetics to geoms and splitting into
subplots - all areas were ease of iteration is vital:
ggraph(graph, 'matrix', sort.by = node_rank_leafsort()) +
geom_edge_point(aes(colour = centrality_edge_betweenness()), mirror = TRUE) +
theme(legend.position = 'bottom')ggraph(graph, 'fr') +
geom_edge_link() +
geom_node_point() +
facet_nodes(~ group_infomap())