Building_Communities: Builds the communities from the set of all data points.
In SamSPECTRAL: Identifies cell population in flow cytometry data.

Description Usage Arguments Value Author(s) References See Also Examples

Some sample points are picked up and the points close to each sample point are considered as members of that community.

1 2	Building_Communities(full, m=3000, space.length=1, community.weakness.threshold=1, talk=TRUE, do.sampling=TRUE, replace.inf.with.extremum=TRUE)

`full`	The matrix containing the coordinates of all data points.
`m`	An integer determining upper and lower bounds on the final number of sample points which will be in range `.95m/2` and 2 `1.1m`
`space.length`	An estimate for the length of a cube that is assumed to contain all data points.
`community.weakness.threshold`	The communities with number of members less than this threshold will be ignored. Normally, setting it to 1 is reasonable.
`talk`	A boolean flag with default value TRUE. Setting it to FALSE will keep running the procedure quite with no messages.
`do.sampling`	A boolean flag with default value TRUE. If set to FALSE, the sampling stage will be ignored by picking up all the data points.
`replace.inf.with.extremum`	If TRUE, the Inf and -Inf values will be replaced by maximum and minimum of data in each direction.

Returns a society which is a list of communities.

Habil Zare and Parisa Shooshtari

Zare, H. and Shooshtari, P. and Gupta, A. and Brinkman R.B: Data Reduction for Spectral Clustering to Analyse High Throughput Flow Cytometry Data. BMC Bioinformatics, 2010, 11:403.

SamSPECTRAL,check.SamSPECTRAL.input

	
	 ## Not run: 
	    library(SamSPECTRAL)

	   # Reading data file which has been transformed using log transform
	    data(small_data)
		full <- small
	
		# Parameters:
		m <- 3000; ns <- 200; sl <- 3; cwt <-1
	
    	# Sample the data and build the communities
    	society <- Building_Communities(full=full,m=m, space.length=sl, community.weakness.threshold=cwt)
	
		# Ploting the representatives:
		plot(full[society$representatives,])

	
## End(Not run)