Create graph for BCRs - Githubissues

snaketron / BcellNet

Tool for network-based analysis of B-cell clonal expansion

MIT License

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Create graph for BCRs #3

Closed GitCJW closed 7 years ago

GitCJW commented 7 years ago

Implement a function which create a graph based on a given set of bcrs and its distances. Nodes represent the bcrs (include the sequence) and edges similarity of two connected nodes. The edge contain the value of distance/similarity.

thatsIch commented 7 years ago

Input:

Patient Name
IGraph Data with all vertices as entry and their distance as edge weight
Edge weight level to hide edges with low weight correlation
Color of vertices

Process:

The weight is normalized where 0 is better and higher is worse
Layout by weight e.g. using layout_with_fr
Detect communities

thatsIch commented 7 years ago

Color can be interpolated via defaults if given two datasets

thatsIch commented 7 years ago

@snaketron About how many vertices can a live dataset contain? This is about scaling the graph to consider different plotting techniques due to size (e.g. if there are so many data entries you might only get one big pile of colored circles)

snaketron commented 7 years ago

@thatsIch Difficult to say. Probably dozens of hub vertices (unique sequences with high occurrence in the dataset) and perhaps hundreds of vertices around each hub.

Was this helpful?

thatsIch commented 7 years ago

@snaketron Yes, thank you very much.

thatsIch commented 7 years ago

rplot

potential plot