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 1.40.5 Index]