Command Line Dialog: network import file with source/target node attributes

[alaa.ba...@gmail.com]

Hello,

I would like to ask how can I set the source node and target node attributes when importing new network into Cytoscape ?

The network import file doesn't list any arguments able to do so. For instance:

network create empty name="test" RootNetworkList=" -- Create new network collection --"

network import file file="/home/john/Documents/test.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 indexColumnSourceInteraction=1 indexColumnTargetInteraction=2 RootNetworkList=test TargetColumnList="shared name"

But I would like to specifiy my attributes when importing these networks. Is there anyway to do that ?

Thanks in advance.

Best regards,
Alaa

[Scooter Morris]

Hi Alaa,

    At this point, you can't unfortunately, although I agree it would be nice if you could.  What if we added a new argument: "columnTypeList" that had a comma separated list of values as follows:

s = source node

t = target node

i = interaction

ea = edge attribute

sa = source node attribute

ta = target node attribute

x = do not import

Would that be helpful?

-- scooter

[alaa.ba...@gmail.com]

Hello scooter,

Thanks a lot for the information. However, I didn't really understand how the new argument could help me. Could you please elaborate what could be done with that the new argument "columnTypeList" ?

To give more information, I got more than 50 networks and I would like to batch import them knowing that they have the same header with source/target nodes attributes. As you already know, its not possible to define these attributes when importing them using the Command Line Dialog. So I have to do them manually which is time consuming.

Thanks in advance.

Regards,
Alaa

[Scooter Morris]

Sure -- imagine this command:

network import file file="/home/john/Documents/test.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" columnTypeList="s,t,sa,sa,sa,sa,sa,ta,ta,ta,ta,ta,x" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 RootNetworkList=test TargetColumnList="shared name"

That would import column 1 as the source, column 2 as the target,
columns 3-7 as source node attributes, columns 8-12 as target node
attributes, and not import column 13.

-- scooter

[alaa.ba...@gmail.com]

Ohhh I see, the columnTypeList doesn't appear in the help section for the network import file. No wonder I missed it.

Thanks a lot for the help scooter !

Best regards,
Alaa

[Scooter Morris]

Hi Alaa,
    Sorry -- it doesn't appear because I haven't implemented it, yet
:-)  The question was whether it would be useful or not (i.e. should I
implement it)?

-- scooter

[alaa.ba...@gmail.com]

Hello Scooter,

My answer is: yes, of course !

I think that's a big help for people like me working on Systems Biology. We have many networks that we would like to analyze and compare. Being able to import a batch of files together with source/target attributes is very useful.

Also, while I was working a while ago with all my networks, I was at one point of merging them. To explain briefly my idea, I have networks with the same name but different conditions. For example:

A_condition1
A_condition2
B_condition1
B_condition2
...
50 names (C, D, E...).

Now, I need to union merge them based on their names so they become
A_condition1+2

That would be a nice implementation to see in Cytoscape in the near future.

Best regards,
Alaa

[Scooter Morris]

OK, I added the new argument.  It will be in Cytoscape 3.7 or you could
download the 3.7-SNAPSHOT nightly build tomorrow.

-- scooter

[alaa.ba...@gmail.com]

Thank you Scooter ! :)

Best regards,
Alaa

[alaa.ba...@gmail.com]

On Wednesday, March 14, 2018 at 1:13:08 AM UTC+1, Scooter Morris wrote:

Hello Scooter,

Today, I tried the new nightly build as you suggested. There are a couple of things I would like to mention.

1. The "Command Line Dialog" doesn't appear in the Tools menu.
2. When executing a script file containing the following command:

network import file
file="/home/john/Documents/test.tsv"

dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t"
firstRowAsColumnNames=true
startLoadRow=1
indexColumnSourceInteraction=1
indexColumnTargetInteraction=2
RootNetworkList=test
TargetColumnList="shared name"

columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"


I get a network with each node self-looping itself.


Best regards,
Alaa

[Scooter Morris]

Hi Alaa,
    OK, a couple of things.  First, in order to get to the command
line, do a "View->Show Automation Panel".  The Command Line dialog is
now more integrated into Cytoscape and is in a new CytoPanel at the very
bottom.    Second, can you send me a copy of "test.tsv" or a portion of
it so I can figure out why you are getting loops?  I certainly don't see
that in my tests.

Thanks, and welcome to the world of being a beta-tester!

-- scooter

[Alaa Badredine]

Hello Scooter,

Thanks for the information on the Command Line Dialog new location. I am joining you a sample of my file for you to test. These are the commands that I have used:

network create empty name="test" RootNetworkList=" -- Create new network collection --" 

network import file file="/home/john/Documents/test.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 indexColumnSourceInteraction=1 indexColumnTargetInteraction=2 RootNetworkList=test TargetColumnList="shared name" columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"

Thanks in advance.

Best regards,

Alaa

[Scooter Morris]

Hi Alaa,
    OK, I've fixed that.  By the way, the two "indexColumn..." arguments are now redundant, so you can just import the network with:

network import file file="/home/john/Documents/test.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"

You only need the RootNetworkList and TargetColumnList if you are importing into an existing root network.  Otherwise a new root network will be created for you automatically.

The fix will be in tomorrow's nightly.

-- scooter

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[Alaa Badredine]

Hello Scooter,

Thanks, I will give it a try for the new nightly build.

Cheers,

Alaa

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[Alaa Badredine]

Hello again Scooter,

I got some good and bad news.

The good news, I can now batch import multiple networks at the same time with the command line. 

The bad news, Cytoscape is messing up the data in the source node attribute, which I have even noticed in the current stable version. I am joining you two screenshots for you to understand better what I mean. As you can see, in Cytoscape, the Log2FC and the P-value of PTN is not the same that is found in the file. I have noticed this issue even in the current Cytoscape when I uploaded the files one by one. Is this something related to "shared name" ? If not, then I believe that this shouldn't be the normal behavior to expect when you upload multiple networks in the same collection. Is there any hotfix for this issue ?

Thanks for your hardwork.

Best regards,

Alaa

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[Alaa Badredine]

Hello,

Are there any news concerning my last post ? Please let me know.

Thanks in advance.

Best regards,

Alaa

[Scooter Morris]

On 03/16/2018 02:49 AM, Alaa Badredine wrote:

Hello again Scooter,

I got some good and bad news.

The good news, I can now batch import multiple networks at the same time with the command line. 

The bad news, Cytoscape is messing up the data in the source node attribute, which I have even noticed in the current stable version. I am joining you two screenshots for you to understand better what I mean. As you can see, in Cytoscape, the Log2FC and the P-value of PTN is not the same that is found in the file. I have noticed this issue even in the current Cytoscape when I uploaded the files one by one. Is this something related to "shared name" ? If not, then I believe that this shouldn't be the normal behavior to expect when you upload multiple networks in the same collection. Is there any hotfix for this issue ?

I'm not seeing that with the data file you sent me.  Can you send me the file that's causing problems?

-- scooter

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[Alaa Badredine]

Hello Scooter,

It's not just one file, when you batch upload multiple networks, you will come across it. Try generating multiple networks with source attributes and upload them. You will notice that the values are messed up. In my case, I am working with more than 50 networks in each collection. I have 5 collections. If you still need files, I can join you samples from my data.

Best regards,

Alaa

[Scooter Morris]

I'll definitely need samples, and the script you are using to read them in.

-- scooter

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[Alaa Badredine]

Hello Scooter,

I have compiled 10 samples from my files for you to test. I am joining also the command line that I have used to import them into Cytoscape. The problem should be reproducible. 

Best regards,

Alaa

[Alaa Badredine]

Oh I forgot to mention one thing that could be a clue for the fix. When you upload the networks using the command provided, look at ACTC1, say in sample 1, 2, 4, 5, the Log2FC_A value would be -2.65026268866323 but in the files are different. I did a quick grep on that value and saw that it was coming from sample 7. Hopefully this information would be useful to you.

Best regards,

Alaa

[Alaa Badredine]

Hello,

Are there any news concerning this issue ?

Best regards,

Alaa

[Scooter Morris]

Sorry -- I haven't had a chance to look at it yet.

-- scooter

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[Alaa Badredine]

Dear Scooter,

No need to apologize, please let me know of any news concerning this issue as it is of urgent matter to our project.

Best regards,

Alaa

On Monday, March 26, 2018 at 6:25:16 PM UTC+2, Scooter Morris wrote:

Sorry -- I haven't had a chance to look at it yet.

-- scooter

On 03/26/2018 01:32 AM, Alaa Badredine wrote:

Hello,

Are there any news concerning this issue ?

Best regards,

Alaa

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[Scooter Morris]

Hi Alaa,
    OK, the problem is that you are reading everything into the same root network.  This will overwrite the data in the same column.  I think you don't want to use a shared root network in this case.  So, I think your command file should look like:

# network create empty name="test" RootNetworkList=" -- Create new network collection --"
network import file file="~/samples/samples_1.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_2.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_3.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_4.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_5.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_6.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_7.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_8.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_9.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"
network import file file="~/samples/samples_10.tsv" dataTypeList="s,s,f,f,f,f,f,f,f,f,f,f,s" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea,ea"


Warning: I just found that something is wrong with the latest 3.7 snapshot, so don't update to a later nightly.  Stick with the one you have.

-- scooter

On 3/29/18 4:49 AM, Alaa Badredine wrote:

Dear Ian,

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[Alaa Badredine]

Hi Scooter,

Thanks for your reply. I would like to know if this is the normal behavior of Cytoscape when you read the samples in the same root network. I don't wish to create a new collection for each sample. For example, I have a set of samples that come from different type of experiments. For each experiment, I want to put these samples together in the same collection. Then, it would be easier for the user to navigate through each samples and compare them from an experiment to another. 

Could you please tell me about the issue you found ? Or at least if it has been fixed now ?

Thanks a lot !

Best regards,

Alaa

[Scooter Morris]

On 04/02/2018 04:27 AM, Alaa Badredine wrote:

Hi Scooter,

Thanks for your reply. I would like to know if this is the normal behavior of Cytoscape when you read the samples in the same root network. I don't wish to create a new collection for each sample. For example, I have a set of samples that come from different type of experiments. For each experiment, I want to put these samples together in the same collection. Then, it would be easier for the user to navigate through each samples and compare them from an experiment to another.

Yes it is expected.  Fundamentally, by design, a collection shares table attributes, at least for shared columns.  It is possible to have columns that are local to individual networks (e.g. the "selected" column is local), but the network importer only supports shared columns.  As a result, as you read in each network, it overwrites the columns from previous networks.  Perhaps something we can think about in the future is adding the capability to create local columns.

Could you please tell me about the issue you found ? Or at least if it has been fixed now ?

There was some rearrangement of the parser code in the most recent snapshot and I was getting backtraces when trying to run your script.  I hope to look into it today.

-- scooter

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[Alaa Badredine]

​​

​Hello everyone,

Sorry to reopen this old post.

Scooter, if you still see this, I would like to ask you a few questions about the nightly build of Cytoscape with the new contents. Could you please confirm if the following questions are true/false ?

1. Can I now import multiple networks in the same root while keeping the attributes of each network without affecting the others (local function of Cytoscape when selecting attribute) ?
   
2. Can I use the command dialog to import multiple network files in the same root while making the attributes to be local ? If yes, what is the command to do it ?

Also, I noticed a weird behavior, I tried to upload a network that had similar lines to the following: 

preferredName_A preferredName_B Type_A Log2FC_A Q-value_A BaseMean_A Impact_A Neighborhood_Score Fusion_Score Phylogenetic_Score Coexpression_Score Textmining_Score Experimental_Score Database_Score Combined_Score

MRPS35 A2ML1 DE 1.06132772737978 1.75625284527198e-06 593.369432512771 0.00 0.00 0.00 0.00 0.00 0.00 0.418 0.00 0.418

with the following command:

network import file file="~/samples/test.txt" dataTypeList="s,s,s,f,f,f,s,f,f,f,f,f,f,f,f" delimiters="\t" firstRowAsColumnNames=true startLoadRow=1 columnTypeList="s,t,sa,sa,sa,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea" indexColumnSourceInteraction=1 indexColumnTargetInteraction=2

and creating the network in the attachments. I think this isn't supposed to be normal unless I made a mistake somewhere in my command line. Could you please correct me if I am wrong ?

Thanks in advance.

Kind regards,

Alaa

[Alaa Badredine]

sorry for the bump.

On Thu, Jul 19, 2018 at 3:21 PM Alaa Badredine <alaa.ba...@gmail.com> wrote:

​​

​Hello everyone,

Sorry to reopen this old post.

Scooter, if you still see this, I would like to ask you a few questions about the nightly build of Cytoscape with the new contents. Could you please confirm if the following questions are true/false ?

1. Can I now import multiple networks in the same root while keeping the attributes of each network without affecting the others (local function of Cytoscape when selecting attribute) ?
   
2. Can I use the command dialog to import multiple network files in the same root while making the attributes to be local ?

Also, I noticed a weird behavior, I tried to upload a network that had similar lines to the following: 

preferredName_A preferredName_B Type_A Log2FC_A Q-value_A BaseMean_A Impact_A Neighborhood_Score Fusion_Score Phylogenetic_Score Coexpression_Score Textmining_Score Experimental_Score Database_Score Combined_Score

MRPS35 A2ML1 DE 1.06132772737978 1.75625284527198e-06 593.369432512771 0.00 0.00 0.00 0.00 0.00 0.00 0.418 0.00 0.418

with the following command:

network import file file="/home/badredda/Documents/Analysis/Samples/our_samples/network/String/2.txt" dataTypeList="s,s,s,f,f,f,s,f,f,f,f,f,f,f,f" delimiters="\t" firstRowAsColumnNames=false startLoadRow=1 columnTypeList="s,t,sa,sa,sa,sa,sa,ea,ea,ea,ea,ea,ea,ea,ea" indexColumnSourceInteraction=1 indexColumnTargetInteraction=2

and creating the network in the attachments. I think this isn't supposed to be normal unless I made a mistake somewhere in my command line. Could you please correct me if I am wrong ?

Thanks in advance.

Kind regards,

Alaa

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Best regards,

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Tel: +33 7 68 94 94 77

 

[Scooter Morris]

On Tuesday, August 7, 2018 at 11:32:28 AM UTC-7, Alaa Badredine wrote:

sorry for the bump.

 

No problem -- I did miss it.

On Thu, Jul 19, 2018 at 3:21 PM Alaa Badredine <alaa.ba...@gmail.com> wrote:

​​

​Hello everyone,

Sorry to reopen this old post.

Scooter, if you still see this, I would like to ask you a few questions about the nightly build of Cytoscape with the new contents. Could you please confirm if the following questions are true/false ?

1. Can I now import multiple networks in the same root while keeping the attributes of each network without affecting the others (local function of Cytoscape when selecting attribute) ?
   

Yes, for each column you can indicate whether this is a Shared or Local column.

2. Can I use the command dialog to import multiple network files in the same root while making the attributes to be local ?

No, we haven't (yet) exposed that through the command line.

-- scooter

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