gradient

[alephreish]

Hello Sarah,

I have also a feature request.

It would be nice to have an option to color edges with weights from continous ranges using linear gradients. For example, here is a plot for the test_*_friends.txt dataset with friendshipstrength colored applying a gradient from 0 (red) to 12 (green)

[sperez8]

I am glad you had fun playing around with Hive Plotter. Different color gradients and color picking options are definitely on the list of features I am working to add to Hive Plotter. I also want to find a good way to color nodes and filter nodes etc...

Let me know if you think of other features that could be useful to interpreting the plots. If you want help/guidance or just want to chat about using Hive Plotter for your data please don't hesitate to contact me! I would be happy discuss the different applications of Hive Plotter to your project.

Sarah

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Sarah Perez Masters of Bioinformatics Candidate University of British Columbia T: 604-842-6751 http://munchaholic.wordpress.com/ https://github.com/sperez8/

On Wed, Sep 17, 2014 at 1:25 AM, har-wradim notifications@github.com wrote:

Hello Sarah,

I have also a feature request.

It would be nice to have an option to color edges with weights from continous ranges using linear gradients. For example, here is a plot for the test_*_friends.txt dataset with friendshipstrength colored applying a gradient from 0 (red) to 12 (green)

[image: gradient] https://cloud.githubusercontent.com/assets/2794008/4300376/cb2b54de-3e43-11e4-8510-d78ff7dc5db3.png

— Reply to this email directly or view it on GitHub https://github.com/sperez8/HivePlotter/issues/2.

[alephreish]

Hi Sarah,

thanks for your response. I hacked your program a bit to get the desired result, and now I have a very nice plot for our next paper! HivePlots has very good potential and I like the general design of the output.

Here is a list of features I needed:

• gradient color assignment for edges;
• color assignment for nodes;
• an option to allow nodes without edges,
• adjustable size for nodes,
• direct output to SVG or other vector-image format.

[My own workarounds to these problems are by no means applicable as working solutions].

[sperez8]

Hi har-wradim,

You hit the spot! All of those features are on my to do list. Unfortunately I won't be able to develop these for a few weeks as other research is currently occupying my time.

Nodes without edges: You are the second person to request this so I modified check_nodes() to only give a warning message, and the nodes should appear normally.

Size of nodes: Do you mean to change the size of all nodes? Yes, this can definitely be an option in the GUI. For now, it's easy to do manually:

1. Open the .html file with a text editor
2. Adjust the parameter <var nodesize = 4>.
3. Save the file and re-open the file in your browser.

Varying the size of different nodes is a bit tricky. On the one hand I can see how it can be useful for certain datasets, on the other hand I think adding another level of encoding will probably end up "crowding" the design of hive plots and make them difficult to interpretation. If this is indeed what you meant than we should discuss the reason for doing so as perhaps there are other alternatives.

SVG output: For now I have been using SVG Crowbar to get an .svg copy of the static hive plot. I will be developing a button directly in the html file to save the hive plot as an svg.

If by workarounds you mean Adobe Illustrator than I feel your pain!

Hope that helps for now :)

Sarah

[alephreish]

Hi Sarah,

Nodes without edges

thanks

Size of nodes

In my case I wanted to change the size globally. I ended up cracking the final svg file: I also wanted to change other properties of the nodes and make their colors depend on another grouping principle.

Adobe Illustrator

No, never! It was basically modifying your code and cracking svg afterwards with a custom xml parser.

[sperez8]

Hi again,

FYI, I remembered now why I had originally developed the check_nodes method to check if all nodes had edges: hive plotter will crash if you try to plot the network using network based measurements (degree, betweeness, etc..) because currently these measurements are calculated on a graph built upon the edges, not the nodes, for simplicity. This can be worked around and I'll let you know when lonely nodes can be plotted again :)

[sperez8]

Graphs with unconnected nodes can now be plotted. Other features coming soon.

Sarah

[sperez8]

Hi har-wradim,

I am closing this issue since Hive Panel Explorer has overcome many problems with Hive Plotter (and does so much more!). Let me know if you ended up using this visualization you made in a publication. I would love to feature it on a page of use cases if that's okay with you.

[alephreish]

Hi Sarah,

my congrats with the progress you are making! Yes, sure, here is our publication: Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans.

[sperez8]

Fantastic figure! Glad it came in handy ;)

Sarah

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Sarah Perez, M.Sc. 604-842-6751 science, communication, education http://munchaholic.wordpress.com/ http://canadiancamel.wordpress.com/ https://github.com/sperez8/

On Thu, Sep 17, 2015 at 1:18 AM, Andrey Rozenberg notifications@github.com wrote:

Hi Sarah,

my congrats with the progress you are making! Yes, sure, here is our publication: Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans http://www.biomedcentral.com/1471-2148/15/142.

— Reply to this email directly or view it on GitHub https://github.com/sperez8/HivePanelExplorer/issues/2#issuecomment-141000495 .