consensusClusterNoPlots {neatmaps}

Consensus Cluster Plus without Plots

Description

consensusClusterNoPlots is a wrapper function for ConsensusClusterPlusthat suppresses the creation of the plots that are created automatically.

Usage

consensusClusterNoPlots(df, link_method, dist_method, max_k, reps, p_var,
  p_net, cc_seed)

Arguments

df

A dataframe of network attributes containing only numeric values. The columns of the dataframe should likely be normalized.

link_method

The agglomeration method to be used for hierarchical clustering. Defaults to the average linkage method. See other methods in hclust.

dist_method

The distance measure to be used between columns and between rows of the dataframe. Distance is used as a measure of similarity. Defaults to euclidean distance. See other options in dist.

max_k

The maximum number of clusters to consider in the consensus clustering step. Consensus clustering will be performed for max_k-1 iterations, i.e. for 2, 3, ..., max_k clusters. Defaults to 10.

reps

The number of subsamples taken at each iteration of the consensus cluster algorithm. Defaults to 1000.

p_var

The proportion of network variables to be subsampled during consensus clustering. Defaults to 1.

p_net

The proportion of networks to be subsampled during consensus clustering. Defaults to 0.8.

cc_seed

The seed used to ensure the reproducibility of the consensus clustering. Defaults to 1.

@author Philippe Boileau , [e-mail]

@importFrom ConsensusClusterPlus ConsensusClusterPlus @importFrom grDevices png dev.off