File import problem in 3.2.0

[Max Allan]

Hi,

I'm a newbie to Cytoscape, so apologies if I'm doing something silly. I've tried to minimise opportunity for silliness by testing in v3.0.0 and v3.2.0.

I tried to follow this guide :
https://archaeologicalnetworks.files.wordpress.com/2013/11/brughmans-2013-network-analysis-with-cytoscape-tutorial.pdf
I get to the stage about loading table data and I get an error : Loading table data Types of keys selected for tables are not matching.

You can either download the sample data from the site above or use my sample data below : 

https://archaeologicalnetworks.wordpress.com/resources/

As a new user I thought I'd strip it back to basics, I created 2 CSV files, one with IDs 1,2,3,4 having some relations with IDs 1,2,3,4 of strong or weak type and then named each entity.

So, network.csv looks like :

1,2,strong
1,3,weak
1,4,weak
2,3,weak
3,4,strong

 And table.csv looks like

1,max
2,ed
3,john
4,roger

If I load them up in v3.0.0, I can successfully map the columns and view a network with names. If I try and follow the same steps in 3.2.0 then I get the same error when loading the table.csv : "Loading table data Types of keys selected for tables are not matching."

Bug or user error??

 

Thanks,

Max

[Tim Hull]

This is a known issue- in 3.2.0, we now read numeric columns as numeric-typed data by default instead of as String-typed data. The problem with that is that the "shared name" column we use as an identifier is always String-typed - leading to a type mismatch. To make this work, right-click on the column used for ID in the import preview panel and manually change the type to String. 

We do plan to address this in a future release - though for now this workaround should work...

Tim

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[Khairul Rizal]

Hi... I am new to Cytoscape,and I am using 3.2.1. I  have the same problem in importing table. I want to add new columns into the existing table. I have tried it by importing new table which includes existing column and the new columns that I want to add (I also tried only with shared name column and one new column only). The Cytoscape identifes duplicate column names, and when I hit the OK botton on the message the Cytoscape starts loading the table data, but it stop there. The new columns never appear on Table Panel.

I have tried to change the ID column type into String as suggested, but it didnt work too. Is there any way I can add new column? Or should I do it manually by adding new column and inputting the data cell by cell? Really need your help. Thanks.

Regards,

Khairul 

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[Tim Hull]

One thing to check is that you're selecting the correct key column and network collection - otherwise the data won't show up in the table. If those are correct, do you get any error messages after pressing import? 

If you're still having problems, do you have any sample data that can help us reproduce the problem?

Tim

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[Khairul Rizal]

Dear Tim,

Thanks for your quick response, and yes...the problem still there. 

I make sure that the key column and network collection are correct (I screenshot the basic operation I went through in the attachment). In the Import setup, I changed the column type of key column into String, and disable unwanted column. As you can see, the result shows that Cytoscape only imported blank columns (only the headings appear).

I also tried to import the table in different computer by downloading and installing the Cytoscape 3.2.0. The result still the same. 

In my previous email, my problem was that the Cytoscape stop working while loading the table. Now, it works but come out with empty column (I think I am bit closer to the solution now). Did I miss something in importing the table? Thanks.

Regards,

Khairul  

Tim

Khairul 

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[Khairul Rizal]

Hi Tim... I can solve the problem now ...so please ignore my previous email.

I suspect it something related with the excel file. I open new excel file, copy the Table into a fresh new worksheet and save it with different file name. Then I imported it into Cytoscape and it worked. Now I can continue my work.

Thanks for your help so far :)

Regards,

Khairul

[Scott McNeill]

Tim,

I am also having trouble importing cvs data.  This fix helped me match the "shared name" like you said.  Thanks for that.

But I have two fields that must have special characters in them causing trouble.  I have stopped out any [, . ' ""] but still have trouble.

Is there a know list of special characters that who'll be removed from a cvs upload into Cytoscape?  Also a way to ecape special characters?

Scott

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[Tim Hull]

What are the special characters that are causing problems?

Tim

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[Barry Demchak]

It sounds like there could be a charset component to this.

 

Cytoscape reads/writes UTF-8 character set, which encodes Unicode, and has specific character formation rules for multi-byte characters. ISO-8859 uses different encodings.

 

It could be that you need to simply read the CSV into an editor that accepts both … reading as ISO-8859 and writing as UTF-8, then using the UTF-8 CSV as input to Cytoscape. We’re thinking of allowing Cytoscape to read CSVs using a user-chosen character set, but so far, Cytoscape reads only UTF-8.

 

The Cytoscape release notes say (slightly obscurely):

File Encoding

On all platforms, all Cytoscape session files recorded since v3.0.1 are encoded in UTF-8 instead of the native language encoding. This makes session files portable between workstations in all locales. Users in Japan, Korea, and China are most affected – existing v3.0.0 or v2.x session files must be translated to UTF-8 using a platform-dependent editor (which most users are already using for this purpose). Users in Europe and the Americas are affected, too, if they use characters beyond the standard ANSI 128 – they can translate to UTF-8 using a platform-dependent editor (e.g., Notepad for Windows).

[Abd Ali]

Hi everyone,

i'm facing that issue on importing data information to nodes of a graph.
I checked my data, with notepad++ i saved it as "utf-8", i tried to change the way i store my data with avoiding blankspace between delimiters and "id" but it's worth.
I really don't know what to do, i tried version 3.20 and 3.2.1 but nothing to do.
Here is an example of what kind of data i'm importing:

network data (just two first are relevant):

1 | 3134 | 485 | 1 | 2
2 | 3134 | 3135 | 3 | 4
3 | 485 | 3136 | 5 | 6
4 | 3136 | 2187 | 7 | 8


node data:
1  |   C_2_23_0  |  BOURG-ARCHAMBAULT  |  160 kVA  |  pfois 51.00 kVA  |  nb_bleu 6  |  nb_jaune 0   |  pcum bleu 66 kVA  |  pcum et 13.20 kVA  |  pcum hiv j  0 kVA  |  pcum
2   |   C_2_23_0  |  LATHUS  |  100 kVA  |  pfois 108.00 kVA  |  nb_bleu 34  |  nb_jaune 0   |  pcum bleu 250 kVA  |  pcum et 50.00 kVA  |  pcum hiv j  0 kVA  |  pcum ete j  0
3   |   C_2_23_0  |  LATHUS  |  50 kVA  |  pfois 24.00 kVA  |  nb_bleu 2  |  nb_jaune 0   |  pcum bleu 24 kVA  |  pcum et 4.80 kVA  |  pcum hiv j  0 kVA  |  pcum ete j  0 kVA   | 
4   |   C_2_23_0  |  LATHUS  |  50 kVA  |  pfois 12.00 kVA  |  nb_bleu 1  |  nb_jaune 0   |  pcum bleu 12 kVA  |  pcum et 2.40 kVA  |  pcum hiv j  0 kVA  |  pcum ete j  0 kVA   | 


thank you very much for reading my question
abdel

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[Scooter Morris]

Hi Abdel,
   Are you getting errors with both the network and table (node attribute) imports?  If so, can you let us know what the errors are?

-- scooter

[Abd Ali]

hi,

no it's just on node attribute imports.
I have no message, it's just that no data are imported to the graph nodes.

[Scooter Morris]

I don't see anything wrong with the data, but you may want to make sure that the key columns (column 1 in both files) are both imported the same.  By default, I think the source node column would be imported as a String, so when you import the node data, you'll need to specifically change the first column to type String.  If that doesn't help, can you send me the full files and I'll try to do the import here to see what might be happening.

-- scooter

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[neha singhal]

Hi Khairul,

I am facing the same problem you have mentioned here. I tried everything u have done. But i am still stuck with addition of a new column for the attribute , but the column is empty. I even tried doing the same thing you did, made a new excel file, but no change.

[Barry Demchak]

Can you share the Excel file with us so we can reproduce the problem???

Barry Demchak -- from my mobile phone

Hi Khairul,

Tim

Khairul 

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[moehn...@gmail.com]

Hi, I am a new user to Cytospace. I used this in 2017 with version 3.51 and it went well. Now, I restarted using again the program with version 3.7.1. The problem is whenever I tried to import the table to column, "where to import Table Data is inactive" . So, all data import goes to an unassigned table. I would like to know why I can not import the data to node table directly. Thank you and looking forward to

Tim

Khairul 

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[Alex Pico]

Hi. Importing data to the Node Table is definitely still supported. It’s probably one of the most commonly used operations in Cytoscape! :)

So, can you provide a sample file and a step-wise description of what you are attempting? It’s hard to tell what step is wrong without a detailed example. Screenshots are helpful as well.

In the meantime, here’s a brief tutorial on how to import node data: https://cytoscape.org/cytoscape-tutorials/protocols/importing-data-from-tables/#/

 - Alex

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[Moe hnin si]

Hello Alex,

Thank you so much for replying my question. 

These are  the steps I followed for the data import.

1. Saved the three column (gene-metabolite-interaction) as three-column table in .txt tab delimited format.

2.  Imported the file as flowing, run the Cytoscape and select“import” from the main menu bar, then locate the previously saved three-column file in .txt format, and import it as
“table” (seen in figure). 

3. To run the plugin locate NetworlAnalyzer in the Tool menu and execute “Analyze Network”. Here is an example figure.

 

I followed these steps and could make several import files and several networks at the same time in 2017, please see the figure.

Now, I did the same steps and I could not make the network directly import from table file. When I tried to import the table file as a network, the window shoes up as unassigned table. Here is the screenshot.

I am so grateful if you could figure it out what's my problem in importing file. My data file is attached here. 

Thank you so much again for your kind help and looking forward to hearing from you,

 

Moe

moe...@wsu.edu

moe.h...@usda.gov

 - Alex

Tim

Khairul 

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[Dawn Apostolakou]

Hello. I believe that what you want to do is import the file as "Network From File". You typically Import->Table when you already have a network(s) and want to add some attributes.

Now if that is not the network you want, but only want the interactions from column 3 "Inter", you could remove all lines without "Inter" before import or select the unwanted edges/interaction and delete them. That would get you a network like this:

Hope this helps,

Dawn

On Wednesday, 27 November 2019 02:31:51 UTC+2, Moe hnin si wrote:

Hello Alex,

Thank you so much for replying my question. 

These are  the steps I followed for the data import.

1. Saved the three column (gene-metabolite-interaction) as three-column table in .txt tab delimited format.

2.  Imported the file as flowing, run the Cytoscape and select“import” from the main menu bar, then locate the previously saved three-column file in .txt format, and import it as
“table” (seen in figure). 

3. To run the plugin locate NetworlAnalyzer in the Tool menu and execute “Analyze Network”. Here is an example figure.

 

I followed these steps and could make several import files and several networks at the same time in 2017, please see the figure.

Now, I did the same steps and I could not make the network directly import from table file. When I tried to import the table file as a network, the window shoes up as unassigned table. Here is the screenshot.

I am so grateful if you could figure it out what's my problem in importing file. My data file is attached here. 

Thank you so much again for your kind help and looking forward to hearing from you,

 

Moe

mo...@wsu.edu

moe....@usda.gov

 - Alex

Tim

Khairul 

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[irt...@uc.cl]

Dear all,

I’m also a newbie to Cytoscape and have encountered a similar problem when importing the nodes table. I have a excel file from which I chose first the edges and consequently (from another sheet) imported the node attributes to the network. I followed all the steps (Chose the “Name” column as key) and got a nodes table where I can only see the headings and not any attribute. At first, only some random cells had the information and after many attempts my result was this: all empty.
Could you help me fix this?

[Alexander Pico]

Can you provide sample data files? We can then respond with specific steps to import those files.

- Alex

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[ISABELA TAPIA HERNANDEZ]

Thank you! This is my data, a super simple social network. 

Best,

On Wednesday, 11 December 2019 16:44:06 UTC, Alex Pico wrote:

Can you provide sample data files? We can then respond with specific steps to import those files.

 - Alex

> On Dec 11, 2019, at 7:20 AM, irtapia via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:
>
> Dear all,
>
> I’m also a newbie to Cytoscape and have encountered a similar problem when importing the nodes table. I have a excel file from which I chose first the edges and consequently (from another sheet) imported the node attributes to the network. I followed all the steps (Chose the “Name” column as key) and got a nodes table where I can only see the headings and not any attribute. At first, only some random cells had the information and after many attempts my result was this: all empty.  
> Could you help me fix this?
>
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[Alex Pico]

Your file worked without any changes. Here’s what I did:

File > Import > Network form file. Picked Edges sheet and defined source and target (screenshot)

File > Import > Table from file. No changes to default settings.

And I got the attached network session file.

Hope this helps!

 - Alex

[Nail Besli]

Hi Alex

Why is disappeared the name of nodes, when zoomed-in network. I need to export to the file in png format as a picture

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On Dec 11, 2019, at 3:14 PM, 'ISABELA TAPIA HERNANDEZ' via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:

Thank you! This is my data, a super simple social network. 

Best,

On Wednesday, 11 December 2019 16:44:06 UTC, Alex Pico wrote:

Can you provide sample data files? We can then respond with specific steps to import those files.

 - Alex

> On Dec 11, 2019, at 7:20 AM, irtapia via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:
>
> Dear all,
>
> I’m also a newbie to Cytoscape and have encountered a similar problem when importing the nodes table. I have a excel file from which I chose first the edges and consequently (from another sheet) imported the node attributes to the network. I followed all the steps (Chose the “Name” column as key) and got a nodes table where I can only see the headings and not any attribute. At first, only some random cells had the information and after many attempts my result was this: all empty.  
> Could you help me fix this?
>
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<Book1Cytoscape.xlsx>

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[Scooter Morris]

Hi Nail,

Cytoscape's network renderer has a default "level of detail" that controls what is shown on the screen so that the network view remains interactive.  When you export the image, that level of detail is set to the maximum so you should be able to see everything, including the name of the nodes.  A hint, however, is that if you don't see it on the screen, when you print it out, the names may be on the image, but might be too small to be legible.  You may need to significantly increase the resolution of the PNG or switch to PDF to be able to actually read the text.

-- scooter

On Thursday, January 30, 2020 at 5:02:30 AM UTC-8, Nail Besli wrote:

Hi Alex

Why is disappeared the name of nodes, when zoomed-in network. I need to export to the file in png format as a picture

On Thu, Dec 12, 2019 at 3:38 AM Alex Pico <alex...@gladstone.ucsf.edu> wrote:

Your file worked without any changes. Here’s what I did:

File > Import > Network form file. Picked Edges sheet and defined source and target (screenshot)

File > Import > Table from file. No changes to default settings.

And I got the attached network session file.

Hope this helps!

 - Alex

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On Dec 11, 2019, at 3:14 PM, 'ISABELA TAPIA HERNANDEZ' via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:

Thank you! This is my data, a super simple social network. 

Best,

On Wednesday, 11 December 2019 16:44:06 UTC, Alex Pico wrote:

Can you provide sample data files? We can then respond with specific steps to import those files.

 - Alex

> On Dec 11, 2019, at 7:20 AM, irtapia via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:
>
> Dear all,
>
> I’m also a newbie to Cytoscape and have encountered a similar problem when importing the nodes table. I have a excel file from which I chose first the edges and consequently (from another sheet) imported the node attributes to the network. I followed all the steps (Chose the “Name” column as key) and got a nodes table where I can only see the headings and not any attribute. At first, only some random cells had the information and after many attempts my result was this: all empty.  
> Could you help me fix this?
>
> --
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<Book1Cytoscape.xlsx>

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[Nail Besli]

Thanks alot. It works

On Thu, Jan 30, 2020 at 6:33 PM Scooter Morris <ssbsm...@gmail.com> wrote:

Hi Nail,

Cytoscape's network renderer has a default "level of detail" that controls what is shown on the screen so that the network view remains interactive.  When you export the image, that level of detail is set to the maximum so you should be able to see everything, including the name of the nodes.  A hint, however, is that if you don't see it on the screen, when you print it out, the names may be on the image, but might be too small to be legible.  You may need to significantly increase the resolution of the PNG or switch to PDF to be able to actually read the text.

-- scooter

On Thursday, January 30, 2020 at 5:02:30 AM UTC-8, Nail Besli wrote:

Hi Alex

Why is disappeared the name of nodes, when zoomed-in network. I need to export to the file in png format as a picture

On Thu, Dec 12, 2019 at 3:38 AM Alex Pico <alex...@gladstone.ucsf.edu> wrote:

Your file worked without any changes. Here’s what I did:

File > Import > Network form file. Picked Edges sheet and defined source and target (screenshot)

File > Import > Table from file. No changes to default settings.

And I got the attached network session file.

Hope this helps!

 - Alex

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On Dec 11, 2019, at 3:14 PM, 'ISABELA TAPIA HERNANDEZ' via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:

Thank you! This is my data, a super simple social network. 

Best,

On Wednesday, 11 December 2019 16:44:06 UTC, Alex Pico wrote:

Can you provide sample data files? We can then respond with specific steps to import those files.

 - Alex

> On Dec 11, 2019, at 7:20 AM, irtapia via cytoscape-helpdesk <cytoscape...@googlegroups.com> wrote:
>
> Dear all,
>
> I’m also a newbie to Cytoscape and have encountered a similar problem when importing the nodes table. I have a excel file from which I chose first the edges and consequently (from another sheet) imported the node attributes to the network. I followed all the steps (Chose the “Name” column as key) and got a nodes table where I can only see the headings and not any attribute. At first, only some random cells had the information and after many attempts my result was this: all empty.  
> Could you help me fix this?
>
> --
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<Book1Cytoscape.xlsx>

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[Meerim Nurbaeva]

Hi,

I am new in using cytoscape.

I am having trouble import my data in cytoscoape 3.8.2.

first it takes so long when i import then after loong long time it writes java memory problems on both windows and macbook 

that is the format of excel i put

then

could you help me to figure out what is the problem..

thank you!

[Alex Pico]

How many rows are in your sheet?  You might try saving the sheet as a csv or tsv file and then try importing that. It should be fast for at least thousands of rows.

If this doesn’t fix it, then could you provide the file so we can try to reproduce the issue?

 - Alex

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