Layout.drl, not that better neither, and I am only at 1000 nodes for now. TKplot offers the abilityof manually moving key vertices and edges for a better view. Programmatically it would be hard to define an exact position for each one of the graph items. Anyway, it is not taking hours until now and I can still cope with it.
Thank you once again for your help. On Thu, Dec 4, 2014 at 10:55 PM, Gábor Csárdi <[email protected]> wrote: > 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 >> >> > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > -- Best Regards Lookman SANNI http://blog.lookouster.org
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