reconstruct_recursive {MultIS}

Apply a clustering algorithm recursively to a given time course.

Description

Apply a clustering algorithm recursively to a given time course.

Usage

reconstruct_recursive(
  readouts,
  method = "kmedoids",
  sim = MultIS::get_similarity_matrix(readouts = readouts, upper = TRUE),
  split_similarity = 0.7,
  combine_similarity = 0.9,
  use_silhouette = TRUE,
  cluster_obj = FALSE
)

Arguments

readouts

The time course for which to find clusters.

method

Either "kmedoids", "kmeans" or any string permitted as a method for stats::hclust.

sim

A similarity matrix used with all methods except "kmeans".

split_similarity

Similarity Threshold. If any two elements within a cluster are below this threshold, another split is initiated.

combine_similarity

After Splitting, a combination phase is activated. If any two elements between two clusters have a similarity higher than this threshold, the cluster are combined.

use_silhouette

If TRUE, silhouette is used to define number of cluster during splitting, otherwise cluster are always split into two new clusters.

cluster_obj

If TRUE, a clusterObject with the readouts, similarity and clustering is returned.

Value

A matrix with two columns: "Clone" and "IS" or if cluster_obj = TRUE a cluster object, which can be used to plot the clustering.