R/plot_visnet.R

In kuppal2/xMWAS: xMWAS: R package for data-integration and differential network analysis

plot_visnet <-
function(sg,df_matrix,main_text="Integrative network",Xname="X",Yname="Y",Zname=NA,Wname=NA,communitymembership=NA,footer=NA,id_mapping_mat=NA,html.selfcontained = TRUE,max.connections.interactive=100,seednum=100,layoutmatrix=NA){
    
    save(id_mapping_mat,file="id.Rda")
    
  
    if(is.na(communitymembership)==TRUE){
        #vis.nodes$color <- V(sg)$color
        
        node_attr_matrix<-cbind(V(sg)$name,V(sg)$shape,V(sg)$color,V(sg)$label.cex,V(sg)$vertex.size)
        
    }else{
        
        
        node_attr_matrix<-cbind(V(sg)$name,V(sg)$shape,sg$palette[communitymembership],V(sg)$label.cex,V(sg)$vertex.size)
        
    }

    
    node_attr_matrix<-as.data.frame(node_attr_matrix)
    colnames(node_attr_matrix)<-c("name","shape","color","label.cex","vertex.size")
    
    nrow_df_matrix<-nrow(df_matrix)

    if(FALSE){
            if(nrow(df_matrix)>100){
                
               
                corweight_temp<-abs(df_matrix[,3])
                ind_top_2000<-order(corweight_temp,decreasing=TRUE)[1:max.connections.interactive]
                # print(paste("Only ",max_connections," connections ranked by strength of association will be plotted.",sep=""))
                
                e=df_matrix[ind_top_2000,c(1:2),drop=FALSE]
                
         
                e <- apply(e, 1, paste, collapse=" --")
                
                df_matrix<-df_matrix[ind_top_2000,,drop=FALSE]
                node_names_top2000<-unique(c(as.character(df_matrix$from),as.character(df_matrix$to)))
                
                # sg <- subgraph(sg,v=unique(c(as.character(df_matrix$from),as.character(df_matrix$to))))
                sg<-graph.data.frame(d = df_matrix, directed = FALSE) #induced.subgraph(sg,which(V(sg)$name %in% c(node_names_top2000)))
                #sg<-subgraph.edges(sg,eids=factor(e))
               
            }
    
    }


    
    #graph.data.frame(d = df_matrix, directed = FALSE)
    
    node_vec<-unique(V(sg)$name)
    graphindnum<-seq(1,length(node_vec))
    node_vec<-cbind(node_vec,graphindnum)
    node_vec<-as.data.frame(node_vec)
    colnames(node_vec)=c("id","graphindnum")
        

    
    id_mapping_mat<-id_mapping_mat[which(id_mapping_mat$Node%in%node_vec[,1]),]
    
    node_vec<-merge(node_vec,id_mapping_mat,by.y="Node",by.x="id")
    node_vec<-node_vec[order(as.numeric(as.character(node_vec$graphindnum))),]
    
    node_vec<-node_vec[,-c(2)]
    
    node_type<-gsub(as.character(node_vec[,1]),pattern="[0-9]*",replacement="")
    
    if(is.na(communitymembership)==FALSE){
        node_vec<-cbind(node_vec,node_type)
        node_vec<-as.data.frame(node_vec)
        
        colnames(node_vec)<-c("id","Community", "Name","type")
    
    }else{
        node_vec<-cbind(node_vec,node_type)
        node_vec<-as.data.frame(node_vec)
        
        colnames(node_vec)<-c("id", "Name","type")
        
    }
    
    
    node_name<-as.character(node_vec$id)
    
    node_name[which(node_vec$type=="X")]<-Xname
    node_name[which(node_vec$type=="Y")]<-Yname
    
    if(is.na(Zname)==FALSE){
        
        node_name[which(node_vec$type=="Z")]<-Zname
    }
    if(is.na(Wname)==FALSE){
        node_name[which(node_vec$type=="W")]<-Wname
    }
    
   
    
    vis.nodes<-node_vec #[,c("id","type")]
    if(is.na(communitymembership)==FALSE){
        vis.nodes$title<-paste("Name: ",node_vec$Name, "<br> Community: ",node_vec$Community,sep="") #paste('<a target="_blank" href="" onclick="return false;" style="background-color:white">',paste("Name: ",node_vec$Name, "<br> Community: ",node_vec$Community,sep=""),'</a>',sep="")
    }else{
        vis.nodes$title<-paste("Name: ",node_vec$Name,sep="") #paste('<a target="_blank" href="" onclick="return false;" style="background-color:white">',paste("Name: ",node_vec$Name,sep=""),'</a>',sep="")
    }
    
     
    node_attr_matrix_sel<-merge(node_attr_matrix,node_vec,by.x="name",by.y="id")
      
     
    
    vis.nodes$shape<-V(sg)$shape
    
   
    
    vis.nodes$label<-V(sg)$name
    vis.nodes$label.cex<-V(sg)$label.cex
    vis.nodes$size=V(sg)$vertex.size
    vis.nodes$borderWidth <- 0.5
    vis.nodes$color.border <- "black"
    
      
	
    if(is.na(communitymembership)==TRUE){
        vis.nodes$color <- V(sg)$color
    
    }else{
        vis.nodes$color<-V(sg)$color #sg$palette[communitymembership]
        
    }
    
    
    vis.links<-df_matrix
    
    vis.links$width <- 1+E(sg)$weight/8 # line width
    
    vis.links$color <- E(sg)$color    # line color
    vis.links$arrows <- "NULL" # arrows: 'from', 'to', or 'middle'
    vis.links$smooth <- FALSE    # should the edges be curved?
    vis.links$shadow <- FALSE    # edge shadow
    
    vis.nodes$group <- node_vec$type
    
    net.width="100%"
    net.height="650px"
    # clips as a circle
    add_shape("triangle",plot=mytriangle) #, clip=shapes("circle")$clip,plot=mytriangle)
    # no clipping, edges will be below the vertices anyway
    add_shape("star", clip=shape_noclip,plot=mystar, parameters=list(vertex.norays=5))

	
    
    
    visnet<-visNetwork(nodes=vis.nodes,edges=vis.links,main=main_text,width=net.width, height=net.height)
    
       
    
    
    if(is.na(communitymembership)==FALSE){
        
        # passing custom nodes and/or edges
       
        lnodes <- data.frame(label =paste(unique(node_vec$type),unique(node_name),sep=""),
        shape = unique(vis.nodes$shape), color = rep("grey",length(unique(node_name))),size=rep(8,length(unique(vis.nodes$shape))),shape.size = rep(50, length(unique(node_name))),font.align="top",font.size=15)
      
        ledges1 <- data.frame(color = c("blue","red"),label = c("-ve correlation", "+ve correlation"), arrows =c("NULL", "NULL"),font.align = "top",size=10,font.size=15,border.bottom=30)
        
        ledges2 <- data.frame(color =unique(vis.nodes$color),label = paste("Community",seq(1,length(unique(vis.nodes$color))),sep=""), arrows =rep("NULL", length(unique(vis.nodes$color))),font.align = "top",size=10,font.size=15,border.bottom=30)
        
        ledges<-rbind(ledges1,ledges2)
        
      

    }else{
        
       
        # passing custom nodes and/or edges
        lnodes <- data.frame(label =paste(unique(node_vec$type),unique(node_name),sep=""),
        shape = unique(vis.nodes$shape), color = unique(vis.nodes$color),size=rep(8,length(unique(vis.nodes$shape))),shape.size = rep(50, length(unique(node_name))),font.align="top",font.size=15)
        
        
          ledges <- data.frame(color = c("blue","red"),label = c("-ve correlation", "+ve correlation"), arrows =c("NULL", "NULL"),font.align = "top",font.size=15,border.bottom=30)
    
   
    }
    
    visnet<-visLegend(visnet, position="left", ncol=1,addNodes = lnodes, addEdges = ledges, useGroups = FALSE,main = list(text = "Legend", style = "font-family:Helvetica;color:blue;font-size:14px;text-align:left;"),stepX=100,stepY=100,width=0.125,zoom=TRUE)
    
   
    visnet<-visOptions(visnet,selectedBy = list(variable=c("type"), multiple=T,style = 'width: 200px; height: 26px;
    background: #f8f8f8;
    color: darkblue'), manipulation = TRUE,highlightNearest =list(hover=TRUE,enabled = T, degree = 1),
    nodesIdSelection = list(enabled = TRUE, style = 'width: 200px; height: 26px;
    background: #f8f8f8;
    color: darkblue;
    '))
    
    
    #if(nrow_df_matrix<100){
    
    
    set.seed(seednum)
    l = layoutmatrix #layout.fruchterman.reingold(sg, weights = (1 -abs(E(sg)$weight)))
    
    visnet<-visIgraphLayout(visnet,layout = "layout.norm", layoutMatrix = cbind(l[,1],(-1)*l[,2]),randomSeed=seednum)
    
    #visnet<-visIgraphLayout(visnet,layout = "layout.norm", layoutMatrix = l,randomSeed=100)
    #}
    
    visnet<-visExport(visnet,type="jpeg",float = "middle", label = "Save network",background="white",style='color: darkred;font-size:14px;font-family:Helvetica;width: 200px; height: 20px')
    
    #visnet<-visInteraction(visnet,navigationButtons = TRUE)
    visnet<-visInteraction(visnet,zoomView = TRUE,keyboard = TRUE, navigationButtons = TRUE)
    
    visnet<-visPhysics(visnet,stabilization = FALSE)
    visnet<-visEdges(visnet,smooth = FALSE)
    
    if(is.na(communitymembership)==TRUE){
    visSave(visnet, file = "interactive.network.html",selfcontained = html.selfcontained)
    }else{
        visSave(visnet, file = "interactive.network.communities.html",selfcontained = html.selfcontained)
        
    }
  return(visnet)
}