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).
plotGraphEdgeAttr(
estimate,
plotStabSelec,
labels,
thres.point,
edgeWeights = NULL,
thres.stab = 0.75,
main = "",
edge.color = "blue",
...
)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.
Set to TRUE if estimate results from the stability
selection procedure. Otherwise, estimate is assumed to be a point
estimate.
Variable labels to be displayed in plot.
Value at which the point estimate should be thresholded,
i.e. edges with coefficients smaller than thres.point are not
displayed.
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.
Indicate the threhold value that was used in the stability selection procedure. Used to determine the width of the plotted edges.
Provide the title of the plot.
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")
Currently not all options of igraph are used; additional
arguments are ignored.