template.tree {flowMatch} | R Documentation

## Plot the hierarchy of samples established while creating a template-tree

### Description

All samples within a template are organized as binary tree. This function plots the hierarchy of samples established while creating a template-tree.

### Usage

      template.tree(object, ...)

### Arguments

`object` | An object of class `Template`. The working examples describe how a template is created from a collection of FC samples.
`...` | Other usual plotting related parameters.

### Value

Returns a tree object of class `hclust` storing the hierarchy of the samples in the template.

### Author(s)

Ariful Azad

### References

Azad, Ariful and Pyne, Saumyadipta and Pothen, Alex (2012), Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry; BMC Bioinformatics, 13 (Suppl 2), S10.

### See Also

`Template`, `create.template`

### Examples

     ## ------------------------------------------------
    ## load data
    ## ------------------------------------------------

    library(healthyFlowData)
    data(hd)

    ## ------------------------------------------------
    ## Retrieve each sample, clsuter it and store the
    ## clustered samples in a list
    ## ------------------------------------------------
    set.seed(1234) # for reproducable clustering
    cat('Clustering samples: ')
    clustSamples = list()
    for(i in 1:length(hd.flowSet))
    {
      cat(i, ' ')
      sample1 = exprs(hd.flowSet[[i]])
      clust1 = kmeans(sample1, centers=4, nstart=20)
      cluster.labels1 = clust1$cluster
      clustSample1 = ClusteredSample(labels=cluster.labels1, sample=sample1)
      clustSamples = c(clustSamples, clustSample1)
    }

    ## ------------------------------------------------
    ## Create a template from the list of clustered samples and plot functions
    ## ------------------------------------------------

    template = create.template(clustSamples)
    summary(template)

    ## plot the tree denoting the hierarchy of the samples in a template
    tree = template.tree(template)

[Package flowMatch version 1.24.0 Index]