computeHclustPlotOrder {CopyNumberPlots} | R Documentation

## computeHclustPlotOrder

### Description

Given the merge matrix of an hclust object, compute a valid ordering of the samples so a dendogram can be plotted with no line crossings.

Note: It's been implemented from scratch but in our experience reproduces exactly the ordering produced by R own ordering algorithm used by hclust.

### Usage

    computeHclustPlotOrder(m)

### Arguments

`m` | (matrix) A merge matrix with 2 columns representing the merges bewteen elements and clusters. The format is described in the documentation of hclust.

### Value

A vector with the ordering of the nodes.

### Examples

    ztree <- matrix(c(0,3,0.1,2,
                      1,4,0.2,2,
                      5,2,0.3,2,
                      6,7,0.4,2),
                      nrow=4)

     hc.tree <- Ztree2Hclust(ztree)
     plot(hc.tree)

     #Set the ordering to a non-correct ordering
     hc.tree$order <- c(1:5)

     #When we plot, we see line crossings
     plot(hc.tree)

     #Compute a correct ordering and replot
     element.order <- computeHclustPlotOrder(hc.tree$merge)
     hc.tree$order <- element.order
     plot(hc.tree)

[Package CopyNumberPlots version 1.3.3 Index]