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ndippy / dynnetwork

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xgmml format question/issue #14

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Hi

When I use  many starts and ends in <node> section, dynnetwork produce huge 
network and don't play it...

<node id="SVC2" level="1" parent="NA" label="SVC2" start="0" end="488">
 <graphics size="0" fill="0" type="VER_ELLIPSE" start="0" end="1"/>
 <graphics size="0" fill="0" type="VER_ELLIPSE" start="1" end="2"/>
 <graphics size="0" fill="0" type="VER_ELLIPSE" start="2" end="3"/>
...
</node>

My network <2k nodes, 488 time series samples , 382 edges -  is attached to 
this issue.

I use this plugin on  macOS newest updated , Cytoscape 3.0.2 newest updated.

Best regards
Robert

Original issue reported on code.google.com by big...@gmail.com on 16 Nov 2013 at 3:39

GoogleCodeExporter commented 8 years ago 
Hi, the error is caused by a typing error in the xgmml file.
If you run Cytoscape from the command line, you will get notified about the 
error and the line at which it occurs.

line 675778:

<edge source="tttttoooo6" target="133772" start="0" end="488"/>

instead of

<edge source="tttttoooo6" target="133772" start="0" end="488"//

Please verify!
Sabina

Original comment by xani...@gmail.com on 17 Nov 2013 at 6:44

GoogleCodeExporter commented 8 years ago

Original comment by xani...@gmail.com on 17 Nov 2013 at 6:47

GoogleCodeExporter commented 8 years ago 
Hi Sabina,

You have right there was mistake in data but this mistake happen at time when I 
prepared data for you.
If you correct this mistake ... data is imported but it is static. 
Data about size/fill/type  (all graphics) is missed...

Can you check and help?

Best regards
Robert

Original comment by big...@gmail.com on 18 Nov 2013 at 12:06

GoogleCodeExporter commented 8 years ago 
Hi Robert,

sure. Another issue that I see is that you are setting the node size to 0:

graphics size="0"

which causes an exception (you can see it if you run Cytoscape from the command 
line) and freezes the app.

Exception in thread "Thread-38" java.lang.IllegalArgumentException: height is 
too small max:359.11316 min:359.11316 center:359.1131591796875 height:0.0

The node size should be always > 0. Do you still get errors if you correct this?

Sabina

Original comment by xani...@gmail.com on 18 Nov 2013 at 5:03

GoogleCodeExporter commented 8 years ago 
ohhhh... and another thing... 

graphics fill="0"

I'm not sure is valid, should be an hex number to be on the safe side:

graphics fill="#000000"

Original comment by xani...@gmail.com on 18 Nov 2013 at 5:07

GoogleCodeExporter commented 8 years ago 
Sabina,

Thank you.

I will have to check it, repair algorithm and come back....

Best regards
robert

Original comment by big...@gmail.com on 18 Nov 2013 at 5:22

GoogleCodeExporter commented 8 years ago 
btw, if you are setting a size 0 because the node does not exist in that 
interval, you leave the interval completely out, such as:

<node id="1" label="1" start="0" end="2">
  <graphics size="10" start="0" end="1"/>
  <graphics size="5" start="1" end="2"/>
</node>

<node id="1" label="1" start="4" end="5">
  <graphics size="5" start="4" end="5"/>
</node>

Original comment by xani...@gmail.com on 18 Nov 2013 at 5:33

GoogleCodeExporter commented 8 years ago 
Sabina,

node size=0 changed to 0.001 , 0 means no utilization but node is a live
graphics fill="0" changed to fill="#000000" 

No import issue now. Network is dynamic :). Thank you.

Question:

As I understand "DynNetwork" plugin is not fully compatible with VizMapper when 
<graphics> is used.
Node label property is mapped by name (  id or label from imported file with 
Passthrought Mapping). 
There is no other   <graphics> attributes :  size , fill type ... available in 
VizMapper.

Is this bug or  I should define  dynamic values via <<att> as in 
dynNetClusters.xgmml example? VizMapper see those attributes very well.

What do you think ? 

Best regards.
Robert

Original comment by big...@gmail.com on 18 Nov 2013 at 7:30

Attachments:

GoogleCodeExporter commented 8 years ago 
cool. 

no it's not a bug, its lazyness, I didn't implement other attributes yet 
although I'm working on a new release of the app...

in practice you can use vizmap to set graphical properties.
Its fine for static attributes. For dynamic attributes it may be unreliable 
though and I suggest you to set them through the xgmml (Cytocscape doesn't 
handle changing attributes very well at the moment).

Is there any attribute they you would like added to the xgmml?
I'll put in the whishlist ;)

Best,
Sabina

Original comment by xani...@gmail.com on 18 Nov 2013 at 8:04

GoogleCodeExporter commented 8 years ago 
Sabina,

God blessing laziness ... sometimes :) ... probably :)

size , fill type ...as included in my example.

Regards, Robert

Original comment by big...@gmail.com on 18 Nov 2013 at 8:15

GoogleCodeExporter commented 8 years ago 
Thanks Robert.
If you have any additional feedback let us know, it's a good time point since 
we are working on the next release.

Sabina

Original comment by xani...@gmail.com on 20 Nov 2013 at 11:11