sota: Self-organizing tree algorithm (SOTA)

In cogena: co-expressed gene-set enrichment analysis

Description

Computes a Self-organizing Tree Algorithm (SOTA) clustering of a dataset returning a SOTA object. This function comes from sota in the clValid package with litter change.

Usage

sota(
  data,
  maxCycles,
  maxEpochs = 1000,
  distance = "euclidean",
  wcell = 0.01,
  pcell = 0.005,
  scell = 0.001,
  delta = 1e-04,
  neighb.level = 0,
  maxDiversity = 0.9,
  unrest.growth = TRUE,
  ...
)

## S3 method for class 'sota'
print(x, ...)

## S3 method for class 'sota'
plot(x, cl = 0, ...)

Arguments

data	data matrix or data frame. Cannot have a profile ID as the first column.
maxCycles	integer value representing the maximum number of iterations allowed. The resulting number of clusters returned by sota is maxCycles+1 unless unrest.growth is set to FALSE and the maxDiversity criteria is satisfied prior to reaching the maximum number of iterations
maxEpochs	integer value indicating the maximum number of training epochs allowed per cycle. By default, maxEpochs is set to 1000.
distance	character string used to represent the metric to be used for calculating dissimilarities between profiles. 'euclidean' is the default, with 'correlation' being another option.
wcell	alue specifying the winning cell migration weight. The default is 0.01.
pcell	value specifying the parent cell migration weight. The default is 0.005.
scell	value specifying the sister cell migration weight. The default is 0.001.
delta	value specifying the minimum epoch error improvement. This value is used as a threshold for signaling the start of a new cycle. It is set to 1e-04 by default.
neighb.level	integer value used to indicate which cells are candidates to accept new profiles. This number specifies the number of levels up the tree the algorithm moves in the search of candidate cells for the redistribution of profiles. The default is 0.
maxDiversity	value representing a maximum variability allowed within a cluster. 0.9 is the default value.
unrest.growth	logical flag: if TRUE then the algorithm will run maxCycles iterations regardless of whether the maxDiversity criteria is satisfied or not and maxCycles+1 clusters will be produced; if FALSE then the algorithm can potentially stop before reaching the maxCycles based on the current state of cluster diversities. A smaller than usual number of clusters will be obtained. The default value is TRUE.
...	Any other arguments.
x	an object of sota
cl	cl specifies which cluster is to be plotted by setting it to the cluster ID. By default, cl is equal to 0 and the function plots all clusters side by side.

Details

The Self-Organizing Tree Algorithm (SOTA) is an unsupervised neural network with a binary tree topology. It combines the advantages of both hierarchical clustering and Self-Organizing Maps (SOM). The algorithm picks a node with the largest Diversity and splits it into two nodes, called Cells. This process can be stopped at any level, assuring a fixed number of hard clusters. This behavior is achieved with setting the unrest.growth parameter to TRUE. Growth of the tree can be stopped based on other criteria, like the allowed maximum Diversity within the cluster and so on. Further details regarding the inner workings of the algorithm can be found in the paper listed in the Reference section.

Please note the 'euclidean' is the default distance metric different from sota

Value

A SOTA object.

data	data matrix used for clustering
c.tree	complete tree in a matrix format. Node ID, its Ancestor, and whether it's a terminal node (cell) are listed in the first three columns. Node profiles are shown in the remaining columns.
tree	incomplete tree in a matrix format listing only the terminal nodes (cells). Node ID, its Ancestor, and 1's for a cell indicator are listed in the first three columns. Node profiles are shown in the remaining columns.
clust	integer vector whose length is equal to the number of profiles in a data matrix indicating the cluster assingments for each profile in the original order.
totals	integer vector specifying the cluster sizes.
dist	character string indicating a distance function used in the clustering process.
diversity	vector specifying final cluster diverisities.

Author(s)

Vasyl Pihur, Guy Brock, Susmita Datta, Somnath Datta

References

Herrero, J., Valencia, A, and Dopazo, J. (2005). A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics, 17, 126-136.

Examples

#please ref the manual of sota function from clValid.
data(Psoriasis)

sotaCl <- sota(as.matrix(DEexprs), 4)

Example output

Loading required package: cluster
Loading required package: ggplot2
Loading required package: kohonen
Warning message:
replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena' 

cogena documentation built on Nov. 8, 2020, 6:54 p.m.