nesthc: Nest hclust objects to containers.

Description

Method to nest nodes in an active RedeR session.

Usage

nesthc(obj, hc, ...)

Arguments

obj

Object of RedPort Class.

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).

Value

Add/change graph objects and plot corresponding hclust object.

Details

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 .
metric: Metric used to cut the hclust object at the top level (Options: "rootdist", "leafdist" or "height"; default="rootdist") .
nmemb: Minimum number of members for a nest (>=2) .
nlev: Maximum number of levels of a nested sequence (default=2) .
grid: Number of rows and cols to lay out graphs in the panel (default = c(2,3)) .
gridScale: Expansion factor of the grid area in the app panel. Options: 0.0 to 100 (default = 75) .
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)) .
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') . 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.

Examples

Run this code


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

#rdp <- RedPort('MyPort') 

## Not run: 
# 
#   calld(rdp)
#   addGraph(rdp,g)
#   nesthc(rdp, hc)
# 
# ## End(Not run)

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