RunModularityClusteringspaceST: Runs the modularity optimizer java program...

In ludvigla/spaceST: spaceST

Description

Runs the modularity optimizer java program (ModularityOptimizer.jar)

Usage

RunModularityClusteringspaceST(SNN = NULL, set.modularity = 1,
  set.resolution = 0.8, set.algorithm = 1, n.start = 100,
  n.iter = 10, random.seed = 0, print.output = FALSE,
  temp.file.location = NULL)

Arguments

SNN	SNN matrix to use as input for the clustering algorithms
set.modularity	Modularity function to use in clustering (1 = standard; 2 = alternative).
set.resolution	Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities.
set.algorithm	Algorithm for modularity optimization (1 = original Louvain algorithm; 2 = Louvain algorithm with multilevel refinement; 3 = SLM algorithm)
n.start	Number of random starts.
n.iter	Maximal number of iterations per random start.
random.seed	Seed of the random number generator
print.output	Whether or not to print output to the console
temp.file.location	Directory where intermediate files will be written.

Value

Seurat object with identities set to the results of the clustering procedure.

ludvigla/spaceST documentation built on May 29, 2019, 3:43 a.m.