The intended use of this function is to visualize a sparsified
precision/partial correlation matrix as an undirected graph. When type
= "plain" a plain undirected graph is given representing the conditional
(in)dependencies exemplified by the sparsified precision.
When type = "fancy" a more elaborate graph is given in which dashed
lines indicate negative partial correlations while solid lines indicate
positive partial correlations, and in which grey lines indicate strong
edges. Strong edges are deemed such by setting cut. If a the absolute
value of a precision element \(\geq\) cut the corresponding edge is
deemed strong and colored grey in the graph. The argument cut is thus
only used when type = "fancy".
When type = "weighted" an undirected graph is given in which edge
thickness represents the strength of the partial correlations. The
nEcolor colored edges then represent negative partial correlations
while pEcolor colored edges represent positive partial correlations.
(Relative) edge thickness in this type of graph can be set by the argument
scale. The arguments scale, nEcolor, and pEcolor
are thus only used when type = "weighted".
The default layout gives a circular placement of the vertices. Most layout
functions supported by igraph are supported (the function is
partly a wrapper around certain igraph functions). The igraph
layouts can be invoked by a character that mimicks a call to a
igraph layout functions in the lay argument. When using
lay = NULL one can specify the placement of vertices with the
coords argument. The row dimension of this matrix should equal the
number of (pruned) vertices. The column dimension then should equal 2 (for
2D layouts) or 3 (for 3D layouts). The coords argument can also be
viewed as a convenience argument as it enables one, e.g., to layout a graph
according to the coordinates of a previous call to Ugraph. If both
the the lay and the coords arguments are not NULL, the lay argument
takes precedence
The legend allows one to specify the kind of variable the vertices
represent, such as, e.g., mRNA transcripts. The arguments label,
Lcex, and PTcex are only used when legend = TRUE.
If prune = TRUE the vertices of degree 0 (vertices not implicated by
any edge) are removed. For the colors supported by the arguments
Vcolor, VBcolor, VLcolor, pEcolor, and
nEcolor see https://stat.columbia.edu/~tzheng/files/Rcolor.pdf.