This function is a wrapper function for plot.igraph, with 2 main additions.
1. Add the ability to color vertices by their attributes (see examples), accompanied by an inofrmative
legend. 2. Resize vertex.size, edge.arrow.size, label.cex according to the plot size and the size of the
network.
plotNetwork(
graph,
vertex.color,
col.palette = palette(),
layout = layout.auto,
legend = TRUE,
...
)Arguments
- graph
An annotated igraph object.
- vertex.color
A list of colors for vertices, or an attribute names (ex: "pathway") by which vertices will be colored. Complex attributes, where a vertex belongs to more than one group, are supported. This can also be the output of
colorVertexByAttr.- col.palette
A color palette, or a palette generating function (ex:
col.palette=rainbow).
- layout
Either a graph layout function, or a two-column matrix specifiying vertex coordinates.
- legend
Wheter to plot a legend. The legend is only plotted if vertices are colored by attribute values.
- ...
Additional arguments passed to
plot.igraph.
Value
Produces a plot of the network.
See also
Other Plotting methods:
colorVertexByAttr(),
layoutVertexByAttr(),
plotAllNetworks(),
plotClassifierROC(),
plotClusterMatrix(),
plotCytoscapeGML(),
plotPathClassifier(),
plotPaths()
Examples
data("ex_kgml_sig")
plotNetwork(ex_kgml_sig, vertex.color="pathway")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...
plotNetwork(ex_kgml_sig, vertex.color="pathway", col.palette=heat.colors)
plotNetwork(ex_kgml_sig, vertex.color="pathway",
col.palette=c("red", "green","blue","grey"))
