Skip to content

A React component to sketch / search for network motifs.

License

Notifications You must be signed in to change notification settings

VCG/vimo-sketches

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

96 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

npm version Demo doi

Vimo Sketches

React component for interactively sketching & searching for network motifs.

Examples

  • Motif analysis in Neuprint. Access here
  • Motif Analysis in Vimo. Access here

Requirements

  • npm (8.1.0 or later)
  • "@testing-library/react": "^12.1.3
  • "react": "^17.0.2"
  • "react-dom": "^17.0.2"

Install Package

npm install @vimo-public/vimo-sketches

Getting Started

Basic Example

import {Sketch} from "@vimo-public/vimo-sketches";
import {useState} from "react";

function App() {
    const [attributes, setAttributes] = useState({
      displayMotifCount: false,
    });

    const processRequest = async (motifJson, lim) => {
        console.log("This function is called upon clicking the search button.");
    };
    return (
        <div>
            <Sketch processRequest={processRequest} attributes={attributes} />
        </div>
    );
}
export default App;

Node & Edge Attributes

If you want to add attributes to nodes or edges, please refer react-awesome-query-builder config fields. Also here's an example

import {Sketch} from "@vimo-public/vimo-sketches";

function App() {

    const attributes = {
        NodeFields: {
            node_attr_1: {
                label: "attr1_name",
                type: "text",
            },
            node_attr_2: {
                label: "attr2_name",
                type: "select",
                fieldSettings: {
                    showSearch: true,
                    listValues: [
                        "alpha",
                        "betha",
                        "theta",
                    ],
                },
                valueSources: ["value"],
                operators: ["select_equals", "select_not_equals"],
            },
        },
        EdgeFields: {
            edge_attr_1: {
                label: "attr1_name",
                type: "number",
                fieldSettings: {
                    min: 0,
                },
                valueSources: ["value"],
                preferWidgets: ["number"],
            },
            edge_attr_2: {
                label: "attr2_name",
                type: "number",
                operators: ["greater", "less", "equal"],
                valueSources: ["value"],
            },
        },
    }
    const processRequest = async (motifJson, lim) => {
        // this function is called when the user clicks the "Search" button
        console.log(motifJson);
        console.log(lim);
    };
    return (
        <div>
            <Sketch processRequest={processRequest} attributes={attributes}/>
        </div>
    );
}

export default App;

Searching Motifs in NeuPrint

We provide a direct interface to sketch & search for networks motifs in large connectome data sets hosted on Neuprint. Here's an example of how to use it.

import React, { useEffect, useState } from "react";
import {Sketch, NeuprintExecutor} from '@vimo-public/vimo-sketches';

function App() {
  const token = "ADD YOUR TOKEN HERE"; // copy token from here https://neuprint.janelia.org/account
  const data_server = "https://neuprint.janelia.org/";
  const data_version = "hemibrain:v1.2.1";
  const vimo_server = "http://127.0.0.1:4242"; // setup instructions https://github.com/VCG/vimo-server
  const ne = new NeuprintExecutor(
    data_server,
    data_version,
    token,
    vimo_server
  );

  const processRequest = async (motifJson, lim) => {
    const query = await ne.json2cypher(motifJson, lim);
    console.log(query);
    return query;
  };

  const [isQuerying, setIsQuerying] = useState(false);
  
  const [attributes, setAttributes] = useState({
      displayMotifCount: false,
      getMotifCount: ne.getMotifCount,
      getRelativeMotifCount: ne.getRelativeMotifCount,
      isQuerying: isQuerying,
  });
  
  useEffect(async () => {
    setAttributes({
      ...attributes,
      NodeFields: await ne.getNodeFields(),
      EdgeFields: await ne.getEdgeFields(),
    });
  }, []);

  return (
    <div>
      <Sketch processRequest={processRequest} attributes={attributes} />
    </div>
  );
}

export default App;

Sketch Component Props

Name Sub-field Description Type
processRequest(query) N/A callback function for search button Function
attributes isQuerying enable/disable search button Boolean
NodeFields constraint fields for node Object
EdgeFields constraint fields for edge Object
getMotifCount get count of motif in network Function
getRelativeMotifCount get relative count of motif in network Function
buttonText text on button, default is "Search" String
nodeColors color set for nodes in sketch, default is ["#9400D3", "#DAA520", "#97d0b5", "#76acf3", "#FF6347", "#4C56B3", "#D9C226", "#263DD9",] Array
  • Token can be found in here.

NeuprintExecutor Parameters

Name Description Type
token neuPrint authentication token String
data_server url of database (e.g., 'https://neuprint.janelia.org/') String
data_version name and version of dataset (e.g., 'hemibrain:v1.2.1') String
vimo_server url of vimo_server (e.g., 'http://localhost:4242') String

Output

This component turns motif sketch into JSON. This is an example of the JSON. This JSON can be converted to a Cypher query using the json2cypher method of the NeuprintExecutor class.

{
    nodes: [
      {
        label: "A",
        properties: null,
        index: 0,
        position: ["Point", 149.70313, 66.80469],
      },
      {
        label: "B",
        properties: null,
        index: 1,
        position: ["Point", 84.70313, 173.80469],
      },
      {
        label: "C",
        properties: null,
        index: 2,
        position: ["Point", 232.70313, 165.80469],
      },
    ],
    edges: [
      {
        label: "A -> B",
        properties: null,
        index: 0,
        indices: [0, 1],
        tree: null,
      },
      {
        label: "B -> C",
        properties: null,
        index: 1,
        indices: [1, 2],
        tree: null,
      },
      {
        label: "C -> A",
        properties: null,
        index: 2,
        indices: [2, 0],
        tree: null,
      },
    ],
    dimension: { width: 639.3984375, height: 232.796875 },
};

Citing

If you find our work helpful, please consider citing it.

@article {troidl2023vimo,
	author = {Troidl, Jakob and Warchol, Simon and Choi, Jinhan and Matelsky, Jordan
    	and Dhanysai, Nagaraju and Wang, Xueying and Wester, Brock and Wei, Donglai
    	and Lichtman, Jeff W and Pfister, Hanspeter and Beyer, Johanna},
	title = {Vimo: Visual Analysis of Neuronal Connectivity Motifs},
	year = {2023},
	doi = {10.1101/2022.12.09.519772},
	publisher = {IEEE},
	URL = {https://www.biorxiv.org/content/10.1101/2022.12.09.519772v2},
	journal = {IEEE Transactions on Visualization and Computer Graphics (IEEE VIS) (to appear)}
}

We gratefully acknowledge the support from NSF award number IIS-2124179.