[R] network plot problem

[Rui Barradas]

Hello,

It's more or less the same it was with vertices. If the edge labels 
represent weights, then create an appropriate attribute and set the 
labels' values to that attribute's values:

E(g)$weight <- something   # keep the weights in a separate attribute
E(g)$label <- E(g)$weight     # set when needed

The plot function now uses these edge labels.

Rui Barradas

Em 28-07-2012 17:44, Vlatka Matkovic Puljic escreveu:
> Is it possible to write a numbers of link next to lines of the network?
>
> For exmple, I have 3 trials that have studied two drugs in network.
> So, now it seems all links are of same weight.
>
>
>
>
>
> 2012/7/27 Vlatka Matkovic Puljic <v.matkovic.puljic at gmail.com>
>
>> Thank you!
>>
>> It works fine now! :)
>>
>>   2012/7/27 Rui Barradas <ruipbarradas at sapo.pt>
>>
>>> Hello,
>>>
>>> As for the directed = FALSE, it works with me:
>>>
>>> g <- graph(given, directed = FALSE)
>>>
>>> As for the label, it's easy. Create an attribute 'name' and then set the
>>> label to that attribute. For instance, using the alphabet's letters, first
>>> uppercase.
>>>
>>> V(g)$name <- c(LETTERS, letters)[V(g)]  # or any other names
>>> V(g)$label <- V(g)$name
>>>
>>> Keep 'name' and 'label' separate, like this you may change the label if
>>> needed but the name will still be there.
>>> Then the plot functions recognise the label attribute.
>>>
>>>
>>> Hope this helps,
>>>
>>> Rui Barradas
>>>
>>> Em 27-07-2012 11:37, Vlatka Matkovic Puljic escreveu:
>>>
>>>>   Thank you Rui.
>>>>
>>>> With matrix works better. I got plot I have expected to have.
>>>>
>>>> I want to be undirected. But
>>>>
>>>> directed = FALSE
>>>> or
>>>> as.undirected(graph)
>>>>
>>>> are not working? Where I'd gone wrong?
>>>>
>>>> Shouldn't it be possible to add names  instead of numbers of nods with
>>>> vertex.label= ?
>>>>
>>>>
>>>>
>>>> 2012/7/26 Rui Barradas <ruipbarradas at sapo.pt>
>>>>
>>>>   Hello,
>>>>> I don't see the problem.
>>>>>
>>>>> given <- scan(text="
>>>>>
>>>>> 15 2
>>>>> 10 4
>>>>> 10 4
>>>>> 10 4
>>>>> 13 4
>>>>> 13 4
>>>>> 15 4
>>>>> 18 4
>>>>> 11 5
>>>>> 2 6
>>>>> 7 6
>>>>> 7 6
>>>>> 7 6
>>>>> 12 6
>>>>> 15 6
>>>>> 15 6
>>>>> 19 6
>>>>> 22 6
>>>>> 24 6
>>>>> 6 7
>>>>> 5 12
>>>>> 5 12
>>>>> 7 12
>>>>> 11 12
>>>>> 13 12
>>>>> 13 12
>>>>> 13 12
>>>>> 13 12
>>>>> 16 12
>>>>> 17 12
>>>>> 23 12
>>>>> 23 12
>>>>> 23 12
>>>>> 23 12
>>>>> 6 13
>>>>> 12 13
>>>>> 6 14
>>>>> 6 15
>>>>> 9 15
>>>>> 12 15
>>>>> 13 15
>>>>> 17 16
>>>>> 16 17
>>>>> 1 18
>>>>> 12 18
>>>>> 23 18
>>>>> 2 19
>>>>> 6 19
>>>>> 24 19
>>>>> 21 22
>>>>> 3 25
>>>>> 5 26
>>>>> 6 27
>>>>> 7 27
>>>>> 15 29
>>>>> 20 30
>>>>> 25 31
>>>>> 28 31
>>>>> 8 32
>>>>> 6 33
>>>>> 14 33
>>>>> 22 34
>>>>> ")
>>>>> mat <- matrix(given, ncol=2, byrow=TRUE)
>>>>>
>>>>> g <- graph(given)
>>>>> # Or, not run (note the transpose)
>>>>> #g <- graph(t(mat))
>>>>> # The edges are exactly what is given
>>>>> E(g)
>>>>>
>>>>> V(g)$label <- V(g)
>>>>> g$layout <- layout.fruchterman.reingold
>>>>> plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE)
>>>>>
>>>>>
>>>>> So my guess is you've messed up the graph creation.
>>>>> Also, don't post datasets like that, use dput(), lik this:
>>>>>
>>>>> dput(given)
>>>>> c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11,
>>>>> 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6,
>>>>> 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13,
>>>>> 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6,
>>>>> 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16,
>>>>> 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25,
>>>>> 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6,
>>>>> 33, 14, 33, 22, 34)
>>>>>
>>>>> Now all anyone has to do is to copy that output and paste it into an R
>>>>> session.
>>>>> (Try it with the matrix to see the result)
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> Rui Barradas
>>>>> Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu:
>>>>>
>>>>>   **Hi,
>>>>>>
>>>>>> I wanted to create a network of drugs that are being studied together.
>>>>>> So, I created a file as a graph.
>>>>>> But plot of my network is not corect!
>>>>>> It looks like to me that something else is lying behind this network
>>>>>> links
>>>>>> created.
>>>>>>
>>>>>> Could someone help me with this?
>>>>>>
>>>>>> Thanx!
>>>>>>
>>>>>> a<-read.graph(file=file.****choose(), format="edgelist")
>>>>>>
>>>>>> plot.igraph(a)
>>>>>>
>>>>>> File (number present ID of drug):
>>>>>>
>>>>>> 15 2
>>>>>> 10 4
>>>>>> 10 4
>>>>>> 10 4
>>>>>> 13 4
>>>>>> 13 4
>>>>>> 15 4
>>>>>> 18 4
>>>>>> 11 5
>>>>>> 2 6
>>>>>> 7 6
>>>>>> 7 6
>>>>>> 7 6
>>>>>> 12 6
>>>>>> 15 6
>>>>>> 15 6
>>>>>> 19 6
>>>>>> 22 6
>>>>>> 24 6
>>>>>> 6 7
>>>>>> 5 12
>>>>>> 5 12
>>>>>> 7 12
>>>>>> 11 12
>>>>>> 13 12
>>>>>> 13 12
>>>>>> 13 12
>>>>>> 13 12
>>>>>> 16 12
>>>>>> 17 12
>>>>>> 23 12
>>>>>> 23 12
>>>>>> 23 12
>>>>>> 23 12
>>>>>> 6 13
>>>>>> 12 13
>>>>>> 6 14
>>>>>> 6 15
>>>>>> 9 15
>>>>>> 12 15
>>>>>> 13 15
>>>>>> 17 16
>>>>>> 16 17
>>>>>> 1 18
>>>>>> 12 18
>>>>>> 23 18
>>>>>> 2 19
>>>>>> 6 19
>>>>>> 24 19
>>>>>> 21 22
>>>>>> 3 25
>>>>>> 5 26
>>>>>> 6 27
>>>>>> 7 27
>>>>>> 15 29
>>>>>> 20 30
>>>>>> 25 31
>>>>>> 28 31
>>>>>> 8 32
>>>>>> 6 33
>>>>>> 14 33
>>>>>> 22 34
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>
>>   --
>> **************************
>> Vlatka Matkovic Puljic
>> gsm: +32.474.894953
>>
>>
>