R/private_plotFGNet.R

In FGNet: Functional Gene Networks derived from biological enrichment analyses

# graph2plot:
# graphCommonGTsets = functionalNetwork (default)
# mgJoinedGraph = intersectionNetwork (bipartite)

plotFGNet <- function(graph2plot, plotType, plotOutput, plotExpression, vertexLayout, eWidth, eColor, vColor, vExpr, vSize, vLabelCex, vShape="circle", colores, markGroup=NULL, trCols=NULL, plotTitle, plotTitleSub, plotLegend, legendPrefix, legendText)
{    
    if(length(vSize)>1)
    {
        # Default value        
        if("default" %in% names(vSize))
        {
            def <- vSize["default"]
            vSize <- vSize[-which(names(vSize)=="default")]
        }else{
            def <- mean(vSize)        
        }
        
        tmpVSize <- rep(def, length(V(graph2plot)))
        names(tmpVSize) <- V(graph2plot)$name
        
        vSize <- vSize[names(vSize)%in% names(tmpVSize)]
        tmpVSize[names(vSize)] <- vSize
        vSize <-tmpVSize
    }
    
    #####################################################################################################
    #########################################  Draw PLOTS  ##############################################
    if(plotOutput=="dynamic")
    {
        # if(is.null(plotIntersectionNetwork)) plotIntersectionNetwork <- TRUE
        if(ecount(graph2plot)>0)
        {
            vBorder <- "#888888"
            if(plotExpression == "fill") vBorder <- sub("#FFFFFF", "#888888", vColor)
            if(plotExpression == "border")
            {
                vBorder <- vExpr
            }
            
            tkplot(graph2plot, layout=vertexLayout, edge.width=eWidth, edge.color=eColor, vertex.label=V(graph2plot)$name, vertex.label.cex=vLabelCex, vertex.label.family="sans", vertex.color=vColor, vertex.size=vSize, vertex.frame.color=vBorder, vertex.label.color="black")  # vertex.label no estaba especificado para intesection network
        } else
        {
            warning("The dynamic plot is not available for networks without edges, try the 'static' plot.", immediate.=TRUE) # Tkplot error: Error in mapply(function(from, to, id) .tkplot.create.edge: zero-length inputs cannot be mixed with those of non-zero length
        }
    }
    if(plotOutput=="static")
    {        
        if(plotType=="bipartite")
        {
            add <- FALSE
            if(plotExpression == "border")
            {
                outerVsize <- vSize+3
                if(length(outerVsize)==1) 
                {
                    outerVsize <- setNames(rep(outerVsize, length(vExpr)), names(vExpr))
                }
                outerVsize[which(vExpr=="#888888")] <- 0
                
                plot(graph2plot, layout=vertexLayout, edge.width=eWidth, edge.color=eColor, vertex.color=vExpr, vertex.frame.color=vExpr, vertex.label="",  vertex.size=outerVsize, vertex.shape=vShape) 
                add <- TRUE
            }
            
        }else # "default" (FunctionalNetwork con background)
        {            
            add <- TRUE
            # Background and border
            if(plotExpression == "fill")
            {
                plot(graph2plot, layout=vertexLayout, edge.width=eWidth, edge.color=eColor, vertex.label="", mark.groups=markGroup, mark.col=trCols, mark.border=colores, vertex.size=0)
            }else
            { # Border or default/false
                if(all(vExpr=="#888888"))
                {
                    outerVsize <- 0
                }else
                {
                    outerVsize <- vSize+3
                    if(length(vSize)>1) outerVsize[which(vExpr=="#888888")] <- 0
                }               
                plot(graph2plot, layout=vertexLayout, edge.width=eWidth, edge.color=eColor, vertex.label="", mark.groups=markGroup, mark.col=trCols, mark.border=colores, vertex.color=vExpr, vertex.frame.color=vExpr, vertex.size=outerVsize)
            }
            
            # Legend
            if(plotLegend) 
            {
                if(!any(is.na(suppressWarnings(as.numeric(names(colores)))))) colorOrder <- order(as.numeric(names(colores)))
                else colorOrder <- order(names(colores))
                legend(-1.35, -1.35, legend=paste(legendPrefix, names(colores)[colorOrder], legendText, sep=""), fill=colores[colorOrder], bty="n", xjust=0, yjust=0)
            }
        }
        if(add) eWidth <-0
        plot(graph2plot, layout=vertexLayout, edge.width=eWidth, edge.color=eColor, vertex.label=V(graph2plot)$name, vertex.label.cex=vLabelCex, vertex.label.family="sans", vertex.color=vColor, vertex.size=vSize, vertex.frame.color=vExpr, vertex.shape=vShape, vertex.label.color="black", add=add)   # en intersect. no estaba vertex.label ni vertex.frame.color=vExpr,
        title(main=plotTitle, sub=plotTitleSub)    
    }
}