cytoscape-helpdesk Google Group

Re: How to edit a file of edge attributes

2009-11-21T10:47:24Z

I was so carless that I forgot to type a white space between the
sourece protein and the open parenthesis.After I corrected the error,I
imported the file successfully.

Re: How to import attribute from a file

2009-11-21T10:43:33Z

I'm so soory.I was so carless that I forgot to insert a white space
between the source protein and the open parenthesis,which made the
file not be read correctly.
Thanks for the patient help.

How to edit a file of edge attributes

2009-11-21T08:38:08Z

I am a new user of cytoscape. I edited a file of node attributes:
primarykey alias expressionstrength
a1 b1 0.3
a2 b2 0.4
a3 b3 0.5
The format is .xls.Then I imported the file sucessfully.But I came
across some problems when I tried to import a file of edge attributes:

Re: How to import attribute from a file

2009-11-19T12:10:23Z

Hi Betty,
I'm replying to your question via the helpdesk list;
as I stated already the id for an edge is in the format
nodeAId [space] (interactiontype) [space] nodeBId
In your primary key column the spaces are lacking:
a1(pp)a2 -> a1 (pp) a2
cheers,
Piet

--
Piet Molenaar
p.molen...@amc.uva.nl

Re: [cytoscape-helpdesk] Re: How to import attribute from a file

2009-11-19T08:41:38Z

Hi,
See here for supported network fileformats;
[link]

By far the easiest way however is to use import>File from Table (text/ms
excel):
[link]

Re: [cytoscape-helpdesk] Re: GML file w/ node coordinates

2009-11-19T01:13:17Z

hey,

i appended two files (due to the 4MB restriction of this mailing list):
yEd.displayed.graph.jpg:export ed graph von yEd
input.graph.gml:the input graph

cheers

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Re: [cytoscape-helpdesk] Re: GML file w/ node coordinates

2009-11-19T00:24:02Z

Can you send us the file in question and perhaps a screenshot of yEd with
what you expect to see?

thanks,
Mike

--
______________________________ ______________________________
Michael Smoot, Ph.D.
UCSD Department of Medicine
tel: 858-822-4756

Re: GML file w/ node coordinates

2009-11-19T00:00:55Z

for smaller gmls it just works fine. whats the matter?

Re: How to import attribute from a file

2009-11-18T23:08:53Z

Hello Bettey and Piet,

I am getting the same problem as Betty is. I do not know how to work
this problem out. I want to color my nodes on the basis of the
interactions strength but is not able to do it. Would be really great
if Piet could you send us a file format which we can download and run

Re: [cytoscape-helpdesk] Re: python scripting

2009-11-18T21:20:58Z

Hi Keiichiro,

Thank you for your earlier response. I'm looking through the javadocs.
Are there more example scripts online or available besides those
listed at the site:

[link]

I may be able to do more if I can see how others have accomplished

Re: [cytoscape-helpdesk] How to import attribute from a file

2009-11-18T15:21:13Z

Hi Betty,
From the manual (
[link]
):

Edge names are all of the form:

sourceName (edgeType) targetName

Specifically, that is

*Table 10. *

sourceName space openParen edgeType closeParen space targetName

How to import attribute from a file

2009-11-18T13:22:30Z

Here is the case:I import a network from the table,but come across a
prolem when I try to import the edge attribution from the file
***.eda.For example,I importe the following network:
a1 pp a2
a2 pp a3
a3 pp a1
a3 pp a3
the fomat of the file above is .xls.
Then I try to import the edge attribution from the file ***.eda.The

Re: [cytoscape-helpdesk] tutorial pages are down

2009-11-16T18:16:47Z

Hi.
Due to a poor user support from the web hosting company (which is
hosting our web pages and wiki), we are planning to migrate wiki to
one of our server. Once we finish the work, we will announce it here.

Sorry for the inconveniences.

Kei

2009/11/15 zikester <isaac...@gmail.com>:

tutorial pages are down

2009-11-16T06:56:04Z

[link]

leads to "internal server error"

GML file w/ node coordinates

2009-11-16T00:33:01Z

Hey,

I have a GML file w/ 12682 nodes and 14703 edges.
when importing in yEd all works fine. but when I try to import it into
cytoscape the coordinates are NOT displayed properly (node and edge
cardinal is correct).

what happened?

thanks
johannes