Query regarding remove duplicates option in edit menu

[AISWARYA JAYAPRAKASH]

Sir,

I have a undirected network A in which few edges are in A-B and B-A format. When I tried to remove such duplicate edges in cytoscape, it's showing result as 30000 edges.

Where as when I do the same operation in using "remove.multiple = true" in igraph R package it's returning me 27381 edges. 

Why such difference is seen in both tools. Which one will be accurate.?

[Alex Pico]

Just to confirm: In Cytoscape, when you perform “Remove Duplicated Edges” you are checking the “ignore edge direction” option?  And in igraph you are performing the `simplify` function with the remove.multiple param set to TRUE on an graph defined as undirected? https://igraph.org/r/doc/simplify.html

These details matter. Please provide alternative steps if my guesses are wrong.

I would expect the two operations I described to be the same. Can you provide a sample network so we can reproduce the scenario?

 - Alex

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CACww5%3DQFXRCnhZZFMRNbR1-sr1jeeP6cyYEnp9DeGENTYVia3w%40mail.gmail.com.

[AISWARYA JAYAPRAKASH]

Sir,

I have checked both options - “ignore edge direction”  and "create an edge table column with a number of duplicate edges" in cytoscape.

And in igraph the code i have used is 

" net<-simplify(gg, remove.multiple = TRUE)" where gg is the network  

It is noted that both igraph and cytoscape remove same no of duplicate edges when a network with 100 edges where 50 edges are A-B type and another 50 edges are B-A type was given as input

But when a network with 100 edges  where 75 edges are A-B type and another 30 edges are B-A type (that means there were 15 edges without any duplicates) were used, igraph is removing duplicate edges as well as self loops whereas cytoscape removes only duplicate edges. This scenario was observed. 

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/9CAE6FCC-D84B-4592-94A7-091A3E39D17D%40gladstone.ucsf.edu.

--

With Regards
Aiswarya Jayaprakash

Ph.D Scholar,

Dr.P.T.V.Lakshmi Lab
Centre For Bioinformatics,
Pondicherry University

[Alex Pico]

Ah, sounds like you found the difference. The simplify function has a parameter “remove.loops” which is TRUE by default. In Cytoscape, we don’t have a “simplify” function that combines these. We have them as separate functions under the Edit menu.

 - Alex

On Mar 12, 2021, at 10:08 PM, AISWARYA JAYAPRAKASH <aiswary...@gmail.com> wrote:

Sir,

I have checked both options - “ignore edge direction”  and "create an edge table column with a number of duplicate edges" in cytoscape.

And in igraph the code i have used is 

" net<-simplify(gg, remove.multiple = TRUE)" where gg is the network  

It is noted that both igraph and cytoscape remove same no of duplicate edges when a network with 100 edges where 50 edges are A-B type and another 50 edges are B-A type was given as input

But when a network with 100 edges  where 75 edges are A-B type and another 30 edges are B-A type (that means there were 15 edges without any duplicates) were used, igraph is removing duplicate edges as well as self loops whereas cytoscape removes only duplicate edges. This scenario was observed. 

On Sat, Mar 13, 2021 at 1:42 AM 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:

Just to confirm: In Cytoscape, when you perform “Remove Duplicated Edges” you are checking the “ignore edge direction” option?  And in igraph you are performing the `simplify` function with the remove.multiple param set to TRUE on an graph defined as undirected? https://igraph.org/r/doc/simplify.html

These details matter. Please provide alternative steps if my guesses are wrong.

I would expect the two operations I described to be the same. Can you provide a sample network so we can reproduce the scenario?

 - Alex

<Screen Shot 2021-03-12 at 12.08.36 PM.png>

On Mar 12, 2021, at 11:07 AM, AISWARYA JAYAPRAKASH <aiswary...@gmail.com> wrote:

Sir,

I have a undirected network A in which few edges are in A-B and B-A format. When I tried to remove such duplicate edges in cytoscape, it's showing result as 30000 edges.

Where as when I do the same operation in using "remove.multiple = true" in igraph R package it's returning me 27381 edges. 

Why such difference is seen in both tools. Which one will be accurate.?

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CACww5%3DQFXRCnhZZFMRNbR1-sr1jeeP6cyYEnp9DeGENTYVia3w%40mail.gmail.com.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/9CAE6FCC-D84B-4592-94A7-091A3E39D17D%40gladstone.ucsf.edu.

--

With Regards
Aiswarya Jayaprakash

Ph.D Scholar,

Dr.P.T.V.Lakshmi Lab
Centre For Bioinformatics,
Pondicherry University

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CACww5%3DQmHsiPDtBEN_1_N%3DoJe920fR1-gVtrdUKoE-pdqi21kQ%40mail.gmail.com.