Package 'ggmGraphEditor'

Advanced Graph Layout Editor for Mixed Graphs

Description

An interactive replacement for ggm::plotGraph using shiny and visNetwork. Allows dynamic node repositioning, handles multiple edge types, and outputs node coordinates.

Usage

graphLayout(
  ggm_matrix,
  dashed = TRUE,
  bidirected_roundness = 0.25,
  Viewer = if (Sys.getenv("RSTUDIO") == "1") "Rstudio" else "browser"
)

Arguments

ggm_matrix	an adjacency matrix for mixed graphs, an igraph object, or a descriptive character vector.
dashed	Logical. If TRUE (default), bidirected edges ⁠<->⁠ are drawn as dashed lines.
bidirected_roundness	Numeric. Curvature of bidirected edges when multiple edges are present. Default is 0.25.
Viewer	character string specifying where to display the Shiny application. Valid options are "Rstudio" (to open it in a native internal window), or "browser" (to open it in the default web browser). If not specified, it automatically detects the environment, defaulting to"Rstudio" inside RStudio and "browser" elsewhere.

Value

A matrix of X and Y coordinates for each node, returned after terminating the Shiny application.

Note

The author acknowledges the help of Google Gemini AI (2026).

Author(s)

Giovanni M. Marchetti

Examples

if (interactive()) {
  amat <- matrix(c(0,1,0, 0,0,1, 0,0,0), 3, 3,
                 dimnames = list(c("A","B","C"), c("A","B","C")))
  coords <- graphLayout(amat)
  print(coords)

  # Generating the adjacency matrix from a vector and plotting
  exvec <- c(
    "b", 1, 2, "b", 1, 14, "a", 9, 8, "l", 9, 11,
    "a", 10, 8, "a", 11, 2, "a", 11, 9, "a", 11, 10,
    "a", 12, 1, "b", 12, 14, "a", 13, 10, "a", 13, 12
  )
  graphLayout(exvec)

  # Plotting from a direct adjacency matrix
  amat2 <- matrix(c(0, 11, 0, 0, 10, 0, 100, 0, 0, 100, 0, 1, 0, 0, 1, 0), 4, 4)
  graphLayout(amat2)

  # A graph with double and triple edges
  G <- structure(c(
      0, 101, 0, 0, 100, 0, 100, 100, 0, 100, 0, 100, 0, 111, 100, 0),
       dim = c(4L, 4L),
       dimnames = list(c("X", "Z", "Y", "W"), c("X", "Z", "Y", "W")))
  graphLayout(G)

  # A graph with 4 edges between two nodes
  G4 <- matrix(0, 2, 2)
  G4[1, 2] <- 111
  G4[2, 1] <- 111
  graphLayout(G4)
}

---

Graph to adjacency matrix

Description

grMAT2 converts graph objects to a mixed adjacency matrix.

Usage

grMAT2(agr)

Arguments

agr

A graph object. This can be: a graphNEL object, an igraph::igraph() object, or a character vector of length $3e$, where $e$ is the number of edges. If it is a vector, it must be a sequence of triples (type, node1label, node2label). The type of edge can be: "a" (arrow from node1 to node2), "b" (bi-directed arc), "l" (undirected line), or "*" (for an isolated node with node1 == node2).

Details

Support for graphNEL objects requires the graph package from Bioconductor, which is a suggested dependency. If the package is missing, passing a graphNEL object will trigger an informative error.

Value

A matrix consisting of 4 different integers representing the $ij$-elements:

• 0 for a missing edge between $i$ and $j$,

• 1 for an arrow from $i$ to $j$,

• 10 for a full line between $i$ and $j$, and

• 100 for a bi-directed arrow between $i$ and $j$. These numbers are added when multiple edges of different types are present. The matrix is symmetric with respect to full lines and bi-directed arrows.

Author(s)

Kayvan Sadeghi, Giovanni Marchetti

Examples

## Generating the adjacency matrix from a vector
exvec <- c(
  "b", 1, 2, "b", 1, 14, "a", 9, 8, "l", 9, 11, "a", 10, 8,
  "a", 11, 2, "a", 11, 10, "a", 12, 1, "b", 12, 14, "a", 13, 10, "a", 13, 12)
grMAT2(exvec)

## Example with graphNEL (requires the 'graph' package from Bioconductor)
if (requireNamespace("graph", quietly = TRUE)) {
  V <- c("a", "b", "c")
  g <- graph::graphNEL(nodes = V, edgemode = "undirected")
  grMAT2(g)
}

g <- c("a", 3, 1, "l", 1, 2, "*", 4, 4)
grMAT2(g)

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