template.tree {flowMatch} | R Documentation |
All samples within a template are organized as binary tree. This function plots the hierarchy of samples established while creating a template-tree.
template.tree(object, ...)
object |
An object of class |
... |
Other usual plotting related parameters. |
Returns a tree object of class hclust
storing the hierarchy of the samples in the template.
Ariful Azad
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.
## ------------------------------------------------ ## 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)