Plot function for S3 class "MixedGraph"

Plot the graph of MixedGraph object using igraph, cytoscape and cytpscape.js.

# S3 method for MixedGraph
plot(x, method = c("igraph", "cytoscape",
  "cytoscape.js"), weighted = FALSE, stability = 0, out.file = NULL, ...)

Arguments

x

is a MixedGraph object.
method

is the related package or lib used in the function. When "igraph", the function will use the R package "igraph". When "cytoscape", the function will use the R package RCy3, the user should start the Cytoscape software before call the function. And when "cytoscape.js", the function will use the lib cytoscape.js.
weighted

is a boolean value, which indicates if we would plot the width of edge according to the weight of edge.
stability

is the stability threshold, when the stability score of the edge is more than it means the coefficient between the two vertices can be trusted.
out.file

is the file name to save the plot of MixedGraph object. The default value is NULL, and the graph will be plotted to the screen.
...

other arguments for different methods.

  • igraphthe generic arguments for plot.igraph is available.

  • cytoscapelayout: the names should be in RCy3::getLayoutNames(CytoscapeWindow), the default layout is "attributes-layout". And you can also modify the layout throungh Cytoscape software.

  • cytoscape.jsTo be extend

Examples

X <- lapply(1 : 3, function(x){matrix(rnorm(12), nrow = 4)})
crf_structure = matrix(c(1, 0, 1, 1, 1, 1, 0, 0, 1), 3, 3)
brail_control <- list(B = 5, tau = 0.6)
G <- MixedGraph(X, crf_structure, brail_control = brail_control)
plot(G, method = "igraph", weighted = TRUE)
plot(G, method = "cytoscape.js", out.file = "./docs/cytoscapejs.html")
#> Create the dir  ./docs 
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in dirname(to): a character vector argument expected