nesthc {RedeR}R Documentation

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.

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).

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 <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.

Value

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

Note

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

Author(s)

Mauro Castro

See Also

RedPort nestNodes gtoy.rm

Examples

# 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)  

[Package RedeR version 1.38.0 Index]