rasmusfonseca / evobundle Goto Github PK

• HiC data
• Protein folding
• Google for time-varying network datasets.

Use a triangle, like a volume in the TV

1- Works when sort
2- Does not animate when we go

Add a big handle for the different clusterings. The handle can be used to hide all nodes/links that does not belong to the clusters.

Eurocup..

Start with 1/32 and make a frame for every countries BUT we want to keep each past frame, with some opacity.

The track will keep growing up and represents the number of victories for a given team.

look at github@openfootball and writes a parser

• Summary plots. Scale thickness to reflect fraction of interactions over entire time period. Transition edge widths to summary
• Adding network centrality measures to external track (degree for now). Transition from cur color to network centrality
• Correlated interactions .. figure out how
• Annotation arc should adapt to label length (See salt bridges example).
• Available and documented scripts to generate JSON files from trajectory and from multi-model pdb.
• Clustering based on strongly connected network components.

• Write MCMC description
• Discuss figures

Hi !

When you click on summarize button, there is a quick flash when we see all the links and then
the widths of all links are updated.

If you look at the DOM, you will see that most of the links are not displayed because they have
a stroke width < 0.2, and so, there are not displayed.

Should we make a scale [minWeight, maxWeight] => [0, maxStrokeWidth=50], so we got a better visual feedback. Because right now, we are hiding links that have weight ?

In addition, i think we should add a key function for the links, that would be the same as the class of the link.. This will allow correct removal/addition/update of link ( or maybe it will change nothing :), but at least a link would be correctly identified).

On hover, color the edges in black

Set up MOR (4dkl/5c1m) example. 1 panel with structure (either pv or png from pymol). 1 panel with interaction-animation. Get play/reverse/forward and "toggle" function working.

Thanks for letting me participating in the project :)

I have a couple of random thoughts there... that comes more from a developer perspective

It looks like the JSON format is ad-hoc/data-set oriented.

What i see there is a graph that evolves over time, so we could have an internal representation that will store the graph and its evolution.
That would decouples our JSON from the chart. Right now it is very tied to the type of chart. I tried to make another type of chart with the same datas to illustrate my point.

And by having a graph representation, you can use all graph representation algorithm ( i give you a simple idea, say the graph is the representation of the interaction of the people of a book... if the graph is a spanning tree at a moment T, we know that all people interact at that 'frame' )

By having a intermediate representation that is decoupled from the type of chart can give us more ideas... if a JSON is too close from a given chart.. it closes a bit your brain.

These are just some random thoughts, so feel free to comment.. :)

Hi Rasmus,

This afternoon, while I was trying to upload a json file, the display did not show up. Following this, when I click on one of the example json links that you have, two plots show up: one plot from the previously uploaded file that did not show up first and another one for the example data. Also when two plots are loaded, the play/stop buttons don't work. I am pasting an example with this issue. Would you be fine with the previous version being up while you are making edits to the code?

Thanks,
AJ

Right now, when we click on a node, we are bought back to the normal state.

When we switch clustering, this guy disappears

Agenda:

• Implement setTrack
• Fixing API and 'external-facing' documentation
  • Wrap in "chart" object. Set up createChart(divname, inputjson)
• setTree swaps orders of edges. Chabbey found a solution. Lets discuss how to integrate that.
• Examples:
  • Test email script.
  • Convert the TOP7 example
• Ensure that rotation is disabled after merging 'treeTrack' branch
• Remove dependency on index.html css. Essentially: Make sure the minimal example looks decent
• ES6 module (?)
• Make sure that createChart takes a json object and not a raw text. Ensure that uploading a json still works.

Try to simulate a defined output to tell what to move

When we switch clustering, the layout 'retains' some space for the old clustering. Try to get rid of these useless space

Sometimes there is a strange behaviour with the slider, dragging does not work until i release the mouse button, and then the slider jumps to the point i released the mouse

We decided to put a lighter tone to the 'hovered' links

Hey Rasmus,

As you may know, we are creating summary plots of Sparkle based by creating a json with just one frame. In this frame, the edges have thickness scaled to their frequency in the simulations. Unfortunately, due to the recent transparency changes that we made the edges are not being seen clearly anymore. Please see below a before after image of the summary plot. Therefore, would it be possible to just include the transparency as a value in the json file or alternatively, have a version of the plot, where the transparency is 0?

• Redesign web layout as discussed
• Json example with tracks and trees filled out (MOR example)
• Slider
• Dial buttons for changing trees and tracks
• Buttons to convert SVG to PNG and download the file

• Clickable edges
• Radio button / dropdown ui for track and tree (cluster) selection.
• Range slider integration and tie to summary

• Currently, when a chord is highlighted by hovering on a node, the highlighting lacks prominence. How about coloring the chord black based on an "on-hover" action on the nodes?

Think about it

Let's try to have a global context and a 'zoom' part

Some examples ther
https://bl.ocks.org/mbostock/2206590

1. Sort on all chart ( - everything is grey )
2. Sort on clusters , colors should go back to make sense
3. Move Sorting buttons under tracks, disable them if tracks are not present

Creates an auto-generated legend..
By clicking on an element, it will show only the selected cluster