nesthc: Nest hclust objects to containers.
In RedeR: Interactive visualization and manipulation of nested networks

Description Usage Arguments Details Value Note Author(s) See Also Examples

Method to nest nodes in an active RedeR session.

1	nesthc(obj, hc, ...)

`obj`	Object of RedPort Class.
`hc`	Either an object of hclust of pvclust class.
`...`	Additional arguments passed to RedeR application; if a "pvclust" object, it also passes arguments for "pvpick" function (e.g. to set the p-value threshold).

Additional arguments:

cutlevel: Numeric value indicating the point where the hclust object should be cut (default = 2). The distance is related to the option 'metric'. For "rootdist" and "leafdist", the cut level is related to the n steps required to get to the root's level or to the leaf's level, respectively (n>=1). For 'height', the cut is related to the corresponding dendrogram height <numeric>.
metric: Metric used to cut the hclust object at the top level (Options: "rootdist", "leafdist" or "height"; default="rootdist") <string>.
nmemb: Minimum number of members for a nest (>=2) <numeric>.
nlev: Maximum number of levels of a nested sequence (default=2) <numeric>.
grid: Number of rows and cols to lay out graphs in the panel (default = c(2,3)) <numeric>.
gridScale: Expansion factor of the grid area in the app panel. Options: 0.0 to 100 (default = 75) <numeric>.
gscale: Expansion factor to set the nest area related to the parents – or related to the app panel. Provided as a vector with three numbers, c(n1,n2,n3): n1 is related to nests at the first level of the hierarchy (i.e. nests rooted to the panel); n2 is related to nests from single branches, and n3 nests from double branches (default = c(30,75,45)) <numeric>.
isAnchor: Logical value; it sets whether to anchor containers in dynamic layouts.
isAssign: Logical value; it sets whether to assign container names to nested nodes.
theme: Some pre-defined nest attributes. Options: 'tm0','tm1','tm2','tm3','tm4','tm5', 'tm6' (default: 'tm6') <string>. Alternatively, it can be a list with customized attributes.
nlinewidth: Line width of a nested series containers.
nfontsz: Label font size a nested series containers.
plothc: Logical value; whether to plot the corresponding hclust object (i.e. dendrogram).
col: A color vector; it is used to color labels in both containers and corresponding hclust object (i.e. dendrogram nodes).
cex: Numeric character expansion factor of dendrogram text and labels.
xlab: A label for the dendrogram x axis.
ylab: A label for the dendrogram y axis.

Add/change graph objects, plot corresponding hclust object, and return corresponding ids.

Prior calling this method invoke RedeR application via XML-RPC server (i.e. 'calld').

Mauro Castro

RedPort nestNodes gtoy.rm

# Initialize igraph
library(igraph)

g <- gtoy.rm()
hc <- hclust(dist(get.adjacency(g)))

#plot(hc)

## Not run: 

  rdp <- RedPort() 
  calld(rdp)
  addGraph(rdp,g)
  ids <- nesthc(rdp, hc)

## End(Not run)