Nothing
#
# FGNET - DEFAULT (genes-genes with background)
#
plotFGNet_default <- function(metagroupsMatrix,gtSetsMatrix, vLayout, plotOutput, plotExpression, eWidth, eColor, vColor, vExpr, vSize, vLabelCex, colores, markGroup, trCols, weighted, plotTitle, plotTitleSub, plotLegend, legendPrefix, legendText)
{
#####################################################################################################
#################################### Create Matrices ###############################################
nGenes <- nrow(metagroupsMatrix)
nMetagroups <- ncol(metagroupsMatrix)
# Gene - Gene edges
nCommonGTsets <- matrix(ncol=nGenes, nrow=nGenes, data=0)
rownames(nCommonGTsets) <- rownames(metagroupsMatrix)
colnames(nCommonGTsets) <- rownames(metagroupsMatrix)
# Counts
nCommonMgroups <- nCommonGTsets
# Fill:
for(gen1 in rownames(metagroupsMatrix))
for(gen2 in rownames(metagroupsMatrix))
{
if(gen1!=gen2) nCommonMgroups[gen1, gen2] <- sum(metagroupsMatrix[gen1,] + metagroupsMatrix[gen2,]==2)
if(gen1!=gen2) nCommonGTsets[gen1, gen2] <- sum(gtSetsMatrix[gen1,] + gtSetsMatrix[gen2,]==2)
}
#####################################################################################################
#################################### Create Graph ###############################################
# weighted=TRUE The name of the edge attribute will be weight.
# weighted=NULL (Unweighted graph. The elements of the adjacency matrix give the number of edges between vertices.)
graphCommonGTsets <- graph.adjacency(nCommonGTsets, weighted=TRUE, mode="undirected", diag=FALSE)
graphCommonMgroups <- graph.adjacency(nCommonMgroups, weighted=NULL, mode="undirected", diag=FALSE)
#####################################################################################################
######################################### Draw PLOTS ##############################################
if(any(plotOutput %in% c("static", "dynamic")))
{
###########################
# Vertex layout
# weighted=NULL (Unweighted graph. The elements of the adjacency matrix give the number of edges between vertices.) -> No parece importar para el layout
vertexLayout <- vLayout
if(is.null(vertexLayout))
{
# Set layout based on the metagroups
if(nMetagroups>1)
{
# (graphCommonMgroups) NOT weigted: place genes with more mg in common closer
graph4layout <- graphCommonMgroups
} else { # If there is only one metagroup, set layout based on the common gene-term sets
graphCommonMgroups <- NA
graph4layout <- graphCommonGTsets
}
if(FALSE)
{
# Parecido a fruchterman reingold, pero apelotona un poco menos los nodos comunes
vertexLayout <- layout.kamada.kawai(graph4layout)
}else
{
# Si son dos grupos separados (no tienen ningun nodo en comun) kamada kawai superpone los dos grupos = MALO
vertexLayout <- layout.fruchterman.reingold(graph4layout)#, area=200000, repulserad=200000*vcount(graph4layout))
}
}
#######################
# Edge weight
if(is.null(eWidth))
{
if(weighted && ecount(graphCommonGTsets)>0)
{
eWidth <- E(graphCommonGTsets)$weight
eWidth <- floor((eWidth/max(eWidth))*5)
if(min(eWidth)<1) eWidth <- eWidth +1
if(min(eWidth) == max(eWidth)) eWidth <- 1
}else eWidth <- 1
}
#######################
# Plot
plotFGNet(graph2plot=graphCommonGTsets, plotType="default", plotOutput=plotOutput, plotExpression=plotExpression, vertexLayout=vertexLayout, eWidth=eWidth, eColor=eColor, vColor=vColor,
vExpr=vExpr, vSize=vSize, vLabelCex=vLabelCex, colores=colores, markGroup=markGroup, trCols=trCols,
plotTitle=plotTitle, plotTitleSub=plotTitleSub, plotLegend=plotLegend, legendPrefix=legendPrefix, legendText=legendText)
}
ret <- list(iGraph=list(commonClusters=graphCommonMgroups, commonGtSets=graphCommonGTsets),
adjMat=list(commonClusters=nCommonMgroups, commonGtSets=nCommonGTsets))
return(ret)
}
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