Log function on Cytoscape doesn't work

[Roberta]

Hi everyone.
I am visualizing networks on Cytoscape from .graphml files. Those files consist basically in lists of amino acids sequences each one with a certain frequency. Now, I would like to visualize the nodes of my network sized as logarithmic frequency-based, but when I try to calculate the log of the frequency from the f(x) command in Cytoscape, it turns into an error (#ERR: can't convert "frequency [,10]" to a number in a call to LOG()).

Do you know have any idea about what is happening?
Please, ask me for further information if I haven't been clear enough.

Thanks!

[Ruth Isserlin]

can you give me a little bit more info.  Are you building the function using the function builder in cytoscape or are you just typing in to a specific column something like this: = LOG($frequency) ?  What is the type on the column Frequency?  Is it a list? (with the error message you got with [10] just makes me think there might be a list somewhere. 

http://manual.cytoscape.org/en/stable/Column_Data_Functions_and_Equations.html

Thanks, 

Ruth 

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[Roberta Amo]

(sorry If this email comes to you in double copy, I am not sure to have sent the first)

Hi Ruth,

thanks for you answer.

What I have is a list, indeed. I actually have several lists all together, each one consists in sequences and each sequence has a frequency. By R, I saved this files as .graphml and then loaded them into cytoscape. The networks are correctly visualized and the data appear with their columns (name, frequency, public/private...) but when I try to transform all the values from the frequency column, it turns into an error (see attached file). 

I have tried in several ways: adding frequency simply as $frequency from the available option (see stamps) or adding it manually trying to type it properly as suggested (frequency [,10]) but those ways don't work.

I am a newbie in this field, so it's very likely that I am doing some very basic mistake!

Thanks very much in advance!

Roberta

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Il giorno ven 23 nov 2018 alle ore 19:27 Ruth Isserlin <ruth.i...@utoronto.ca> ha scritto:

can you give me a little bit more info.  Are you building the function using the function builder in cytoscape or are you just typing in to a specific column something like this: = LOG($frequency) ?  What is the type on the column Frequency?  Is it a list? (with the error message you got with [10] just makes me think there might be a list somewhere. 

http://manual.cytoscape.org/en/stable/Column_Data_Functions_and_Equations.html

Thanks, 

Ruth 

On Fri, Nov 23, 2018 at 8:51 AM Roberta <roberta....@gmail.com> wrote:

Hi everyone.
I am visualizing networks on Cytoscape from .graphml files. Those files consist basically in lists of amino acids sequences each one with a certain frequency. Now, I would like to visualize the nodes of my network sized as logarithmic frequency-based, but when I try to calculate the log of the frequency from the f(x) command in Cytoscape, it turns into an error (#ERR: can't convert "frequency [,10]" to a number in a call to LOG()).

Do you know have any idea about what is happening?
Please, ask me for further information if I haven't been clear enough.

Thanks!


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[Alex Pico]

Here are the steps for using the Function Builder:

1. Create new column in the Node Table (click on plus sign): New Single Column > Floating Point

2. Name the new columns whatever you want

3. Click into a cell in that new column

4. Click on Function Builder

5. Select Log

6. Pulldown the column you want (e..g, frequency); click Add

7. Type ’10’ into next field down; click Add

8. Confirm that the equation looks right

9. Select Apply to Entire Column

10. Click OK.

Does this work for you?

Note, you can also do this calculation in R and then load the data into Cytoscape.

 - Alex

On Nov 23, 2018, at 2:20 PM, Roberta Amo <roberta....@gmail.com> wrote:

(sorry If this email comes to you in double copy, I am not sure to have sent the first)

Hi Ruth,

thanks for you answer.

What I have is a list, indeed. I actually have several lists all together, each one consists in sequences and each sequence has a frequency. By R, I saved this files as .graphml and then loaded them into cytoscape. The network are correctly visualized and the data appear with their columns (name, frequency, public/private...) but when I try to transform all the values from the frequency column, it turns into an error (see attached file). 

I have tried in several ways: adding frequency simly as $frequency from the available option (see stamps) or adding it manually trying to type it properly as suggested (frequency [,10]) but those ways don't work.

I am a newbie in this field, so it's very likely that I am doing some very basic mistake!

Thanks very much in advance!

Roberta

Mail priva di virus. www.avast.com

Il giorno ven 23 nov 2018 alle ore 19:27 Ruth Isserlin <ruth.i...@utoronto.ca> ha scritto:

can you give me a little bit more info.  Are you building the function using the function builder in cytoscape or are you just typing in to a specific column something like this: = LOG($frequency) ?  What is the type on the column Frequency?  Is it a list? (with the error message you got with [10] just makes me think there might be a list somewhere. 

http://manual.cytoscape.org/en/stable/Column_Data_Functions_and_Equations.html

Thanks, 

Ruth 

On Fri, Nov 23, 2018 at 8:51 AM Roberta <roberta....@gmail.com> wrote:

Hi everyone.
I am visualizing networks on Cytoscape from .graphml files. Those files consist basically in lists of amino acids sequences each one with a certain frequency. Now, I would like to visualize the nodes of my network sized as logarithmic frequency-based, but when I try to calculate the log of the frequency from the f(x) command in Cytoscape, it turns into an error (#ERR: can't convert "frequency [,10]" to a number in a call to LOG()).

Do you know have any idea about what is happening?
Please, ask me for further information if I haven't been clear enough.

Thanks!


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