I am an intermediate level Python user and have recently been using igraph to visualize netweoks and calculate useful properties. I also have experience with Bokeh a Python module that helps render interactive plots with zoom in/out, hover, nodes selection features. How do i pass an igraph into Bokeh or another such module to make more interactive graphs? Thank u very much!
Sent from my iPhone > On Feb 17, 2017, at 12:05 PM, "[email protected]" > <[email protected]> wrote: > > Send igraph-help mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.nongnu.org/mailman/listinfo/igraph-help > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of igraph-help digest..." > > > Today's Topics: > > 1. misplaced edges in fixed layout (Leroi, Armand M) > 2. Re: misplaced edges in fixed layout (George Vega Yon) > 3. Subgraph (Perrone, Alexander G.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Feb 2017 20:22:57 +0000 > From: "Leroi, Armand M" <[email protected]> > To: "[email protected]" <[email protected]> > Subject: [igraph] misplaced edges in fixed layout > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I am using a fixed layout. Under some circumstances, the behaviour of the > edges appears to interact with vertex.size in an unfortunate way > > Below is an example. Here, the default vertex size (15?) gives almost > invisible vertices. But the edges and arrow heads all line up nicely. So, I > increase the vertex.size = 300. Now they?re visible, however, some of the > edges no longer run from vertex-to-vertex. They?re misplaced and pointing in > the wrong direction. This phenomenon seems to affect y-axis-stacked nodes > most acutely. Can anyone suggest a fix? Below is a MWE. Play around with > vertex.size and you should see what I mean. > > With thanks > > Armand > > > > > > > nodes <- c('a','b','c','d','e','f') > x <- c(1540, 1540, 1540,1580,1600,1650) > y <- c(52, 53, 55,56,54,58) > from <- c('a','a','a','a','e','d') > to <- c('b','c','d','e','f','f') > Nodelist <- data.frame(nodes, x ,y) > Edgelist <- data.frame(from, to) > a<- graph_from_data_frame(vertices = Nodelist, d= Edgelist, directed = TRUE) > plot(a, ylim=c(52,58), xlim=c(1530,1650), asp=0, rescale=FALSE, axes=TRUE, > vertex.size=400) > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/b3705e56/attachment.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: smallnodes.pdf > Type: application/pdf > Size: 111734 bytes > Desc: smallnodes.pdf > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/b3705e56/attachment.pdf> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: bignodes.pdf > Type: application/pdf > Size: 111725 bytes > Desc: bignodes.pdf > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/b3705e56/attachment-0001.pdf> > > ------------------------------ > > Message: 2 > Date: Thu, 16 Feb 2017 13:37:30 -0800 > From: George Vega Yon <[email protected]> > To: Help for igraph users <[email protected]> > Subject: Re: [igraph] misplaced edges in fixed layout > Message-ID: > <capjuxxwm8bwxusw1n9k7tbbuqx2pgeffkhadn4exv1gbpne...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Here is a dirty solution using the netdiffuseR package. In particular, I > use the function edges_coords which computes edges coordinates considering > device size and vertices size in terms of the x axis... is not as flexible > as igraph.plotting, but it solves your issue... Will work on a better > solution for the future! > > rm(list =ls()) > library(netdiffuseR) > library(igraph) > > nodes <- c('a','b','c','d','e','f') > x <- c(1540, 1545, 1540,1580,1600,1650) > y <- c(52, 53, 55,56,54,58) > from <- c('a','a','a','a','e','d') > to <- c('b','c','d','e','f','f') > Nodelist <- data.frame(nodes, x ,y) > Edgelist <- data.frame(from, to) > a <- graph_from_data_frame(vertices = Nodelist, d= Edgelist, directed = > TRUE) > > # Getting edge coordinates > vcex <- runif(nnodes(as_adj(a)), 1, 4) > ecoords <- edges_coords( > as_adj(a), > rep(10L, nnodes(as_adj(a))), > x = x, y = y, > vertex_cex = vcex, > dev = par("pin"), no_contemporary = FALSE, > undirected = FALSE > ) > > ecoords <- as.data.frame(ecoords) > > # Plotting > symbols(x, y, circles=vcex, > inches=FALSE, xaxs="i", yaxs="i") > > with(ecoords, arrows(x0,y0,x1,y1, length=.1)) > > Best, > > George G. Vega Yon > +1 (626) 381 8171 <(626)%20381-8171> > http://cana.usc.edu/vegayon > > On Thu, Feb 16, 2017 at 12:22 PM, Leroi, Armand M <[email protected]> > wrote: > >> Hello, >> >> I am using a fixed layout. Under some circumstances, the behaviour of >> the edges appears to interact with vertex.size in an unfortunate way >> >> Below is an example. Here, the default vertex size (15?) gives almost >> invisible vertices. But the edges and arrow heads all line up nicely. So, >> I increase the vertex.size = 300. Now they?re visible, however, some of >> the edges no longer run from vertex-to-vertex. They?re misplaced and >> pointing in the wrong direction. This phenomenon seems to affect >> y-axis-stacked nodes most acutely. Can anyone suggest a fix? Below is a >> MWE. Play around with vertex.size and you should see what I mean. >> >> With thanks >> >> Armand >> >> >> >> >> >> >> nodes <- c('a','b','c','d','e','f') >> x <- c(1540, 1540, 1540,1580,1600,1650) >> y <- c(52, 53, 55,56,54,58) >> from <- c('a','a','a','a','e','d') >> to <- c('b','c','d','e','f','f') >> Nodelist <- data.frame(nodes, x ,y) >> Edgelist <- data.frame(from, to) >> a<- graph_from_data_frame(vertices = Nodelist, d= Edgelist, directed = >> TRUE) >> plot(a, ylim=c(52,58), xlim=c(1530,1650), asp=0, rescale=FALSE, axes=TRUE, >> vertex.size=400) >> >> >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/3f7c6ffe/attachment.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Rplot01.png > Type: image/png > Size: 12040 bytes > Desc: not available > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/3f7c6ffe/attachment.png> > > ------------------------------ > > Message: 3 > Date: Thu, 16 Feb 2017 22:26:06 +0000 > From: "Perrone, Alexander G." <[email protected]> > To: "[email protected]" <[email protected]> > Subject: [igraph] Subgraph > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Is there a way to take the induced_subgraph or delete_vertices by modifying > the graph in place? That is, do not make a copy of the original or create a > new one from scratch? I'm trying to take the k-core of a graph but vast > majority of time is *not* the function coreness(g) but rather creating the > new graph and I'm not interested in the original. > > > Alex > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.nongnu.org/archive/html/igraph-help/attachments/20170216/4ee99a14/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > ------------------------------ > > End of igraph-help Digest, Vol 126, Issue 1 > ******************************************* _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
