[igraph] Making interactive graphs via Bokeh

[Shekhar]

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, "address@hidden" <address@hidden> wrote:
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> 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" <address@hidden>
> To: "address@hidden" <address@hidden>
> Subject: [igraph] misplaced edges in fixed layout
> Message-ID: <address@hidden>
> 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)
> 
> 
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> ------------------------------
> 
> Message: 2
> Date: Thu, 16 Feb 2017 13:37:30 -0800
> From: George Vega Yon <address@hidden>
> To: Help for igraph users <address@hidden>
> Subject: Re: [igraph] misplaced edges in fixed layout
> Message-ID:
>    <address@hidden>
> 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 <address@hidden>
> 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
>> address@hidden
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>> 
>> 
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> ------------------------------
> 
> Message: 3
> Date: Thu, 16 Feb 2017 22:26:06 +0000
> From: "Perrone, Alexander G." <address@hidden>
> To: "address@hidden" <address@hidden>
> Subject: [igraph] Subgraph
> Message-ID: <address@hidden>
> 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
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