Regarding GO data

[gulia...@gmail.com]

Hi, I am Citu and I have the annotation data for my nodes like molecular function,biological process and cellular compartment. I want to import these also in my network externally to the node but I am not able do it. Can I do this using Cytoscape?

Thanks

[Alex Pico]

Yes, of course. You did not describe your data file, but assuming it’s something like this…

Gene GO term

------- -------------

ABC1 kinase activity

ABC2 signaling pathway

… …

Then you can use the table import option to load the terms as annotations mapped via a common column of symbols (like above) or identifiers. A particular column needs to be in common between your data file and your network nodes to serve as a mapping key.

You can load one term per column (like above) or a list of terms per column. Those options are all exposed during the table import dialog.

See this chapter of the manual for details:

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

 - Alex

On Oct 20, 2018, at 4:26 PM, gulia...@gmail.com wrote:

Hi, I am Citu and I have the annotation data for my nodes like molecular function,biological process and cellular compartment. I want to import these also in my network externally to the node but I am not able do it. Can I do this using Cytoscape?

Thanks

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[Citu]

Thanks

My file is in excel format like ist column is the node and subsequent columns are GO data like cellular component , molecular function.  I am able to import the table in cytoscape but do not know how to write these function adjacent to the node. 

Please help me. 

Thanks

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[Alex Pico]

So, you were able to load the annotations into Cytoscape? You can see your annotations in the Table Panel in Cytoscape?  Now your question is how to display the annotations as text placed next to the nodes in the network diagram?

There’s an app for that!

http://apps.cytoscape.org/apps/enhancedgraphics

You will need to add a new “string” column to your Node Table Panel. Call it “label” for example. And add this text to it:

label: attribute=goterms labelsize=10 outline=false background=false color=black dropShadow=false

Replace “goterms" with the name of the column in your network that contains your imported GO terms. After entering the text,  right-click on that entry and choose “Apply to entire column”. This will copy it all nodes.  You can see all the options in the text string for how it is displayed. If you want to change any of those (e.g., labelsize=12), then you can simply change one and then repeat the “Apply to entire column” to update all of them.

Now you have to set the visual property to use this new “label” column:

In the Style Panel, click on the mapping cell for “Image/Chart 1”. Choose the “label” column and choose “passthrough” mapping. 

Now you should see your extra labels displayed. To position them relative to the node, you have to edit another visual property:

Under the properties pull down at the top of the Style Panel, choose “Paint > Custom Paint 1 > Image/Chart Position 1”. 

Go to the newly displayed property and click on the default cell. Move things around and play with the x,y offsets until you like the position.

Done!

A description of all the options for the label type of enhanced graphic is available here:

http://www.rbvi.ucsf.edu/cytoscape/utilities3/enhancedcg.shtml

Good luck!

 - Alex

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[Alex Pico]

Here are some screenshot to accompany the instructions...

 - Alex

[Citu]

Thanks for your help. 

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