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Using Your Own Graph Data

Atlas and the Atlas Edge Decomposition Algorithm use plain text edge lists where sources adn targets are numbers as input. For edge lists with labels instead of numbers, see adding Vertex Labels.

Say your edge list is named myGraph.txt. To use your own graph data, create the new directory data/myGraph.

This directory will contain all the data needed to load your graph into Atlas.

Inside of data/myGraph place the following files:

myGraph-positions.csv contain x and y coordinates for each vertex in your graph. The file should have three columns: the vertex ID, x coordinate, and the y coordinate. You can obtain coordinates from any graph layout of your choosing (for large graphs, we use a GPU layout). If your graph had only three vertices, then your file would look like this:

1,811.958,-217.099
2,737.26,-173.93
3,559.598,-165.009

With these three files, change directories to data-processing:

cd data-processing/

Now run

./data-processing myGraph

data-processing.sh is a bash script that simply calls Python scripts to generate .json files to be read by Atlas.

Once data-processing.sh is finished, you should now have one file called myGraph.json with metadata about your graph, and one .json file for each layer from the decomposition. These files will be named myGraph-layer-X.json where X is the layer number from the decomposition.

All that is left to do is point Atlas at this directory. To do so, open js/index.js, uncomment the current graph being used, and add yours:

// comment out old graph
// const dataDirName = 'lesmis';

// add your new graph data
const dataDirName = 'myGraph';

You are all done! Run Atlas as you normally would. For instructions, see github.com/fredhohman/atlas.

Vertex Labels

Bonus: if you have vertex labels associated with your graph, include a file called myGraph-map.json that is a dictionary whose keys are vertex IDs (numbers) and values are the vertex labels. The file should look like this (if your graph has 3 vertices):

{
	"1": "Euclid",
	"2": "Pythagoras",
	"3": "Archimedes",
}

Once you have run data-process.sh from above, run the following command to add the labels to your .json data:

python add-vertex-labels.py -data myGraph

Example Graph Data

We've included a complete example of a graph to be visualized in Atlas as an example to follow. You can find it in data/lesmis.

Contact

For questions or support open and issue or contact Fred Hohman.