plotGraphEdgeAttr {backShift} R Documentation

## Plotting function to visualize directed graphs

### Description

Given a point estimate of the connectivety matrix or the adjacency matrix, this function visualizes the directed graph using `plot.igraph` from the package `igraph`. If a point estimate is plotted, the edges' intensity reflects the magnitude of the coefficients. If the result is an adjacency matrix estimated by stability selection then the edges' width reflects how often an edge was selected and the intensity reflects the magnitude of the coefficients (if this information is also provided).

### Usage

```plotGraphEdgeAttr(
estimate,
plotStabSelec,
labels,
thres.point,
edgeWeights = NULL,
thres.stab = 0.75,
main = "",
edge.color = "blue",
...
)
```

### Arguments

 `estimate` Estimate of connectivity matrix. This can be a point estimate with entry A_{ij} being the estimated edge weight for the edge from node i to node j. Otherwise, it can be the estimated adjacency matrix by a stability selection procedure as in `backShift`. In this case, the entry A_{ij} indicates how often the edge from node i to node j was selected. `plotStabSelec` Set to TRUE if `estimate` results from the stability selection procedure. Otherwise, `estimate` is assumed to be a point estimate. `labels` Variable labels to be displayed in plot. `thres.point` Value at which the point estimate should be thresholded, i.e. edges with coefficients smaller than `thres.point` are not displayed. `edgeWeights` If stability selection result should be visualized, provide edgeWeights as a (pxp)-matrix to display the magnitude of the coefficients as the intensity of the edges. `thres.stab` Indicate the threhold value that was used in the stability selection procedure. Used to determine the width of the plotted edges. `main` Provide the title of the plot. `edge.color` Color of the edges. Defaults to blue. `...` Optional arguments passed to the plotting function. Consists of igraph-type options like vertex.label.cex,vertex.label.color, edge.arrow.size or vertex.size etc. @examples # create a matrix A to be visualized p <- 3 A <- diag(p)*0 A[1,2] <- 0.8 A[2,3] <- -0.8 A[3,1] <- 0.8 # add column names to use as labels for nodes colnames(A) <- c("1", "2", "3") # plot plotGraphEdgeAttr(estimate = A, plotStabSelec = FALSE, labels = colnames(A), thres.point = 0, thres.stab = NULL, main = "True graph")

### Details

Currently not all options of `igraph` are used; additional arguments are ignored.

[Package backShift version 0.1.4.3 Index]