Re: [igraph] Named vertexes from imported adjacency matrix

[Szabolcs Feczak]

Ive just realized that I made a mistake in the conversion

the ncol format should have double the weights because 

in the directed version
nodes have two edges going back and forth with the same weight

so in undirected format 
that equals to one edge between the nodes with the sum of the weights 
which is exactly double because of the symmetry 

ikon.DEV fors.DEV 18
ikon.DEV matt.DEV 10
astr.DEV matt.DEV 12
astr.DEV ikon.DEV 70
dark.EXT ikon.DEV 10
inca.EXT ikon.DEV 10
inca.EXT astr.DEV 14
ossm.DEV ikon.DEV 10

I have also realized, that my csv import loaded the graphs
with multiple edges so instead of weights and single or double edges
the resulted graph has as many edges as much the sum of the weights,
so I assume each nodes were connected with a number of edges equal
to the weights hm

at least I got it straight now so g.summary() gives the right number of edges

On Sun, Jun 1, 2008 at 3:19 PM, Szabolcs Feczak <address@hidden> wrote:

Hi

Meanwhile I made progress after reading the slim document and guessing
around for 5 hours :D

so some of my questions I can answer myself, but some remain

it works, however meanwhile Im trying to do the same with the python interface
as I might have to do batch processing and it seems to be easier that way

How would I do the same thing in python ?

well I do not know how would I make the same result from the same input,
but I have converted my input file into ncol format and than I could read it much easier

so from my original csv

,fors.DEV,matt.DEV,ikon.DEV,astr.DEV,dark.EXT,inca.EXT,ossm.DEV
fors.DEV,0,0,9,0,0,0,0
matt.DEV,0,0,5,6,0,0,0
ikon.DEV,9,5,0,35,5,5,5
astr.DEV,0,6,35,0,0,7,0
dark.EXT,0,0,5,0,0,0,0
inca.EXT,0,0,5,7,0,0,0
ossm.DEV,0,0,5,0,0,0,0

I made this

ikon.DEV fors.DEV 9
ikon.DEV matt.DEV 5
astr.DEV matt.DEV 6
astr.DEV ikon.DEV 35
dark.EXT ikon.DEV 5
inca.EXT ikon.DEV 5
inca.EXT astr.DEV 7
ossm.DEV ikon.DEV 5


and I could read it easily with

g=Graph.Read_Ncol("ncol", names=True, weights=True, directed=False)

however I have realized that it works a bit different and the Adjacency function ignores non numeric values
so I had to edit the csv by hand and remove the first column and the first row

 
the above conversion method eliminated this problem as well

also, how would I display the weights on the graphs
what I would like to achieve is something like this

http://feczo.nmi.rulez.org/sna/2232.png

it would be nice to have both the line width and the frequencies

I could make the widths:
weights = [edge["weight"] for edge in g.es]
max_weight = max(weights)
g.es["width"] = [1+9*(weight/max_weight) for weight in weights]


but I still do not know how to plot the numeric
values of the weights onto the image
Is this possible ?

Another question popped up meanwhile,
how would I set the margin on the output ?

I have tried
plot(g,target="out.png",layout="reingold_tilford_circular",vertex_label=g.vs["name"],vertex_label_color="#FF4400",bbox=(0,0,960,620),margin=(10,10,10,10))

no luck

also how would I modify the position of the labels ?
 
so actually Im close to what I would like
http://feczo.nmi.rulez.org/sna/13833.png

now I have
http://feczo.nmi.rulez.org/sna/13833-2.png

Would it be possible to give a white or light gray background to the vertex labels so they would cover the lines behind them
to make it much easier to read the labels ?

or even opacity would be nice, I have seen that there is possibility to print layers on the canvas gradually with different opacity
however I could not figure out how would I print the labels and the rest of the image separately

for those who seek working examples of python code with igraph I put down the whole code here for future reference
generating  http://feczo.nmi.rulez.org/sna/13833-2.png from the above input matrix
note: you need the cairo python library for png output


from igraph import *

g=Graph.Read_Ncol("ncol", names=True, weights=True, directed=False)

weights = [edge["weight"] for edge in g.es]
max_weight = max(weights)

color = ["#003300", "#006600", "#009900", "#00CC00", "#00FF00",
        "#33FF00", "#66FF00", "#99FF00", "#CCFF33", "#CCFF00",
        "#000033", "#000066", "#000099", "#0000CC", "#0000FF",
        "#330033", "#660066", "#990099", "#CC00CC", "#FF00FF",
        "#330000", "#660000", "#990000", "#CC0000", "#FF0000"]

g.es["width"] = [1+9*(weight/max_weight) for weight in weights]
g.es["color"] = [color[int(round(24*weight/max_weight))] for weight in weights]
g.vs["size"] = [10+20*cent for cent in g.evcent()]
g.vs["color"] = ["lightblue" for i in g.vs]

plot(g,target="out.png",layout="reingold_tilford_circular",vertex_label=g.vs["name"],vertex_label_color="#FF4400",bbox=(0,0,960,620))



My questions still:

is it possible to measure Freeman node betwenness of the graph ?
to see in how many percentage does it compare to a perfect star ...

 

is it possible to get the standard deviation of the average produced by Graph.density() ?

Thanks

S.