How can I display a title of a network next to its visualization?

[katja...@gmail.com]

Hello,

I am using py2cytoscape to load multiple networks from a jupyter notebook into cytoscape, set the style and layout and then save an image of every network as pdf. I would like to add a title to every image on top (or bottom, doesn't matter) of the network visualization that indicates the name of the network. How can I do that? The networks all have the right name in the network control panel but how can I add these names to the network visualization and saved image?

Many thanks in advance for your help.

Best,
Katja

[Ruth Isserlin]

Hi Katja,
You can manually add an annotation to the network (right click where you want to put the title and add—>annotation and specify the title) with its title before exporting the image but unfortunately I don’t think annotations are accessible through commands yet so you can’t do it automatically with py2cytoscape. In my notebooks when I insert an image I often specify the title from the notebook instead.
Ruth

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[Katja Luck]

Hi Ruth,

Thanks for your quick answer. I didn't know about the right click feature. I just tried it and it worked but sadly I would need automation as I am dealing with 30 and more networks at a time. I don't fully understand your second solution with respect to adding a title from the notebook. You mean when you show the image within the notebook you can add a title and save it then? Would you have some sample code for me starting from my code below?

from py2cytoscape.data.cyrest_client import CyRestClient
cy = CyRestClient()
network = cy.network.create_from_igraph(g,name='network1') # g is some igraph object
pdf = network.get_pdf()
target = open('some_file_path_and_name.pdf','wb')
target.write(pdf)
target.close()

Thanks!
Katja

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[Ruth Isserlin]

HI Katja,
Unfortunately I am not using py2cytoscape. I am using R notebooks. So I am not quite sure how you can do it in your notebook but there should be a way.

In R I simply export the network to a file and then insert the image with something like this:

### Title of figure
```{r example_heatmap, echo=FALSE, fig.cap=“caption for example"}
knitr::include_graphics(example_hetmap_filename)
```

Thanks,
Ruth

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[Scooter Morris]

Hi Katja,

   It's on our project list to provide a connection to the Cytoscape graphical annotations via py2cytoscape, but it didn't make the 3.7 cut-off.  Hopefully we'll be able to add it in 3.7.1 or 3.8.

-- scooter

[Katja Luck]

Ok, thanks!

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