Plot paths between resources

plotPath provides a visual of a graph and the selected path.

plotPath(graph, ...)

# S4 method for class 'igraph'
plotPath(
  graph,
  by = NULL,
  k = 1,
  include = NULL,
  exclude = NULL,
  res.name = NULL,
  focus = FALSE
)

Arguments

graph

An igraph object.

...

Unused.

by

A formula specifying the path to plot. (Default: NULL)

k

Numeric scalar. The kth shortest path to plot. (Default: 1)

include

Character vector. Nodes to cross in the path. (Default: NULL)

exclude

Character vector. Nodes to avoid in the path. (Default: NULL)

res.name

Character vector. Names of resources to include in the graph. (Default: NULL)

focus

Logical scalar. Whether the edges and nodes in the path should be plotted. (Default: FALSE)

Value

A ggplot2 object.

Examples

# Retrieve resource graph
graph <- ariadne()

# Plot graph for a subset of resources
plotPath(graph, res.name = c("KEGG", "WoL"))
#> Warning: Using alpha for a discrete variable is not advised.


# Plot fifth path from ko to ec
plotPath(graph, ko ~ ec, k = 5)
#> Warning: Using alpha for a discrete variable is not advised.


# Plot first path including uniref90
plotPath(graph, taxname ~ ko, include = "uniref90")
#> Warning: Using alpha for a discrete variable is not advised.


# Plot first 5 paths excluding uniref50 and uniref100
plotPath(graph, taxname ~ ko, k = 5, exclude = "uniref50")
#> Warning: Using alpha for a discrete variable is not advised.