We don't have your data, so we cannot run this. Plotting 20000 vertices with tkplot does not make much sense. If you really want to plot them, then use plot() to plot to a file.
The FR algorithm is not a good idea for these networks, either, as it does not scale very well. Maybe layout.drl is better. Gabor On Thu, Dec 4, 2014 at 4:50 PM, lookman sanni <[email protected]> wrote: > I am doing something like the below in one of my plots: > > library(igraph) > > message("Select the edges list") > > el=read.csv(file.choose(),sep="|") > > el=as.matrix(el) > > g = graph.edgelist(el[,1:2],directed=FALSE) > > E(g)$Entries_Count = as.numeric(el[,4]) > > E(g)$Entry_Type = el[,3] > > E(g)$color = E(g)$Entry_Type > > E(g)$color = gsub("164","EType1",E(g)$color) > > E(g)$color = gsub("165","EType1",E(g)$color) > > E(g)$color = gsub("EType1","deepskyblue",E(g)$color) > > E(g)$color = gsub("EType2","orange",E(g)$color) > > E(g)$color = gsub("EType3","gray",E(g)$color) > > E(g)$color = gsub("EType4","green",E(g)$color) > > E(g)$color = gsub("EType5","red",E(g)$color) > > E(g)$color = gsub("EType6","blue",E(g)$color) > > E(g)$color = gsub("EType7","black",E(g)$color) > > message("Select the vertices list") > > nodeinfo=read.csv(file.choose(),sep="|") > > V(g)$Actor_Type = > as.character(nodeinfo$Type[match(V(g)$name,nodeinfo$Name)]) > > V(g)$Actor_Status = > as.character(nodeinfo$status[match(V(g)$name,nodeinfo$Name)]) > > V(g)$shape = V(g)$Actor_Type > > V(g)$shape =gsub("NType1","none",V(g)$shape) > > V(g)$shape =gsub("NType2","sphere",V(g)$shape) > > V(g)$shape =gsub("NType3","pie",V(g)$shape) > > V(g)$color=V(g)$Actor_Status > > V(g)$color=gsub("FormNType1","green",V(g)$color) > > V(g)$color=gsub("FormNType2","gray",V(g)$color) > > V(g)$color=gsub("FormNType3","orange",V(g)$color) > > mySize = V(g)$Actor_Type > > mySize = gsub("NType1","20",mySize) > > mySize = gsub("NType2","0",mySize) > > mySize = gsub("NType3","0",mySize) > > V(g)$size = as.numeric(mySize) > > V(g)$label.cex = 20 > > tkplot.fit.to.screen(tkplot(g, vertex.shape=V(g)$shape, > layout=layout.fruchterman.reingold,vertex.label=NA),width = NULL, height = > NULL) > > > > I will be happy to learn any possible optimization of this. > > Regards > > > On Thu, Dec 4, 2014 at 12:33 PM, lookman sanni <[email protected]> > wrote: > >> Sure...Will be doing that by the end of the day. No access at the moment >> to the hosting machine. >> >> On Thu, Dec 4, 2014 at 12:16 PM, Gábor Csárdi <[email protected]> >> wrote: >> >>> Can you please show the code that is slow? >>> >>> Gabor >>> >>> On Thu, Dec 4, 2014 at 6:07 AM, lookman sanni <[email protected]> >>> wrote: >>> >>>> I have been using the default plot, and also Tkplot for a graph of 1K >>>> nodes, but with very low density (Less than 10 nodes having a significant >>>> local density actually). It takes between 3 and 5 minutes. I should however >>>> recognize that I am not using the appropriate material for that (an HP >>>> Envy). >>>> >>>> On Thu, Dec 4, 2014 at 11:45 AM, Gábor Csárdi <[email protected]> >>>> wrote: >>>> >>>>> So subgraph.edges is slow for you? How long does it take? >>>>> >>>>> Gabor >>>>> >>>>> On Thu, Dec 4, 2014 at 5:09 AM, lookman sanni <[email protected]> >>>>> wrote: >>>>> >>>>>> I was not meaning, but rather fearing it may be. I will be dealing >>>>>> with networks of 20K nodes and 7 layers(subgraphs). I just need to make >>>>>> sure that I am making the most from the optimization opportunities that >>>>>> may >>>>>> exist. >>>>>> >>>>>> Thank you Fatemeh for the links. I will be looking into that as well. >>>>>> >>>>>> Regards, >>>>>> >>>>>> On Mon, Dec 1, 2014 at 5:25 PM, Fatemeh a <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> I searched a little some times ago on Multilayered network : you may >>>>>>> find them helpful : >>>>>>> >>>>>>> http://arxiv.org/pdf/1309.7233v4.pdf >>>>>>> >>>>>>> http://arxiv.org/pdf/1407.0742.pdf >>>>>>> >>>>>>> and here : http://muxviz.net/ a framework is developed to deal >>>>>>> with multilayered network : I didn't work with it and I have no idea >>>>>>> whether you could combine these two package or not. >>>>>>> >>>>>>> Regards, >>>>>>> Fatemeh >>>>>>> >>>>>>> >>>>>>> On Sat, Nov 29, 2014 at 1:52 AM, lookman sanni <[email protected] >>>>>>> > wrote: >>>>>>> >>>>>>>> Hello everyone. I am new to SNA and learning how to use the igraph >>>>>>>> package. I have built a multiplex network from some flat file and would >>>>>>>> like to compute couple of metrics on top of that network: >>>>>>>> >>>>>>>> - The number of edge types by node (multiplexity) >>>>>>>> - A metric (matrix, contingent table) of edge types association >>>>>>>> between the same nodes (e.g: money transfer + good transfer: 20 >>>>>>>> pairs of >>>>>>>> nodes; money transfer + kinship: 120 pairs of nodes) >>>>>>>> >>>>>>>> I have not seen any likely metrics in my web searches. Would I need >>>>>>>> to write them ? If yes, is there any available guideline on how to >>>>>>>> contribute to igraph ? >>>>>>>> >>>>>>>> -- >>>>>>>> Best Regards >>>>>>>> >>>>>>>> Lookman SANNI >>>>>>>> http://blog.lookouster.org >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> igraph-help mailing list >>>>>>>> [email protected] >>>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> regards >>>>>>> F..A >>>>>>> >>>>>>> _______________________________________________ >>>>>>> igraph-help mailing list >>>>>>> [email protected] >>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Best Regards >>>>>> >>>>>> Lookman SANNI >>>>>> http://blog.lookouster.org >>>>>> >>>>>> _______________________________________________ >>>>>> igraph-help mailing list >>>>>> [email protected] >>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> igraph-help mailing list >>>>> [email protected] >>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>>> >>>>> >>>> >>>> >>>> -- >>>> Best Regards >>>> >>>> Lookman SANNI >>>> http://blog.lookouster.org >>>> >>>> _______________________________________________ >>>> igraph-help mailing list >>>> [email protected] >>>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>>> >>>> >>> >>> _______________________________________________ >>> igraph-help mailing list >>> [email protected] >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >>> >> >> >> -- >> Best Regards >> >> Lookman SANNI >> http://blog.lookouster.org >> > > > > -- > Best Regards > > Lookman SANNI > http://blog.lookouster.org > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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