getCyGraphs: getCyGraphs

In mheffe3/SCNVC: Generates Single Cell Networks that can be used in Cytoscape

Description

Calls all the functions necessary to get the functional modules from the Seurat data and PValues and then graphs in Cytoscape.

Usage

getCyGraphs(SData, Ps,NSLB = 100, EWLB = 0.05, cnames = NULL)

Arguments

SData	A Seurat object containing preprocessed data
Ps	Pvalues containing the Pvalues for each gene in the clusters
NSLB	Lower bound for Node Score filtering
EWLB	Lower Bound For Edge Weight filtering
cnames	A list containing names for each of the clusters. Defaults to NULL and uses C1, C2... instaed

Value

No return value instead creates a filtered and unfiltered network in Cytoscape for each cluster

Note

Requires Cytoscape to be opened and installed. Calls getClusterList, getFM, getEdgeWeightsG, GraphInCytoscape, and CyFilter

Author(s)

Matt Heffernan, University of Illinois at Chicago

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

getCyGraphs(SData=SData, Ps=Ps,NSLB = 100, EWLB = 0.05, cnames = NULL)

## The function is currently defined as
function(SData, Ps,NSLB = 100, EWLB = 0.05, cnames = NULL)
{
  countTable <- SData[["RNA"]]@data
  CList <- getClusterList(SData, Ps, cnames)
  FMList <- list()
  i = 0
  for(c in CList)
  {
    pValues <- c$p_val
    names(pValues) <- c$gene
    FMList[[paste("FM", as.character(i),sep="")]] <- getFM(pValues)
    i = i+1
    
  }
  networkList <- list()
  i = 0
  for(f in FMList)
  {
    networkList[[paste("N", as.character(i),sep="")]] <- getEdgeWeightsG(f,countTable)
    i = i+1
    
  }
  
  i = 1
  nClusters <- length(CList)
  hasnames = TRUE
  if(is.null(cnames) || length(cnames) != nClusters)
  {
    hasnames = FALSE
  }
  while(i <= nClusters)
  {
    if(hasnames)
    {
      GraphInCytoscape(FMList[[i]], name=cnames[i])
      CyFilter(FMList[i], name=cnames[i], NSLB = NSLB, EWLB = EWLB)
      
    }
    else
    {
      GraphInCytoscape(FMList[[i]], name=paste("C", as.character(i-1), sep=""))
      CyFilter(FM, name=paste("C", as.character(i-1), sep=""), NSLB = NSLB, EWLB = EWLB)
    }
    
    i = i+1
  }
  
}

mheffe3/SCNVC documentation built on Dec. 21, 2021, 5:52 p.m.