https://github.com/connectome-neuprint/vimo-sketches

A react component of the vimo sketching interface.

https://github.com/connectome-neuprint/vimo-sketches

Repository

A react component of the vimo sketching interface.

https://github.com/connectome-neuprint/vimo-sketches/blob/main/

[![npm version](https://img.shields.io/npm/v/@vimo-public/vimo-sketches.svg?color=1a8cff)](https://www.npmjs.com/package/@vimo-public/vimo-sketches)
[![Demo](https://img.shields.io/badge/demo-running-blue.svg?colorB=4AC8F4)](https://neuprint.janelia.org/?dataset=manc%3Av1.0&qt=motifquery&q=1)
[![doi](https://img.shields.io/badge/doi-10.1109%2FTVCG.2017.2745978-purple.svg?colorB=C46CFD)](https://doi.org/10.1101/2022.12.09.519772)


# Vimo Sketches
React component for interactively sketching & searching for network motifs.


  



### Examples
* Motif analysis in Neuprint. Access [here](https://neuprint.janelia.org/?dataset=manc%3Av1.0&qt=motifquery&q=1)
* Motif Analysis in Vimo. Access [here](https://github.com/jakobtroidl/neuronal-motifs)

### Requirements
* [npm](https://www.npmjs.com/) (8.1.0 or later)
* ```"@testing-library/react": "^12.1.3```
* ```"react": "^17.0.2"```
* ```"react-dom": "^17.0.2"```

### Install Package
``` bash
npm install @vimo-public/vimo-sketches
```

### Getting Started

#### Basic Example
```javascript
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 (
        

            
        
    );
}
export default App;
```

#### Node & Edge Attributes
If you want to add attributes to nodes or edges, please refer react-awesome-query-builder [config fields](https://github.com/ukrbublik/react-awesome-query-builder/blob/master/CONFIG.adoc#configfields). Also here's an example

````javascript
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 (
        

            
        
    );
}

export default App;
````

#### Searching Motifs in NeuPrint

We provide a direct interface to sketch & search for networks motifs in large [connectome](https://en.wikipedia.org/wiki/Connectomics) data sets hosted on [Neuprint](https://neuprint.janelia.org). Here's an example of how to use it.

```javascript
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 (
    

      
    
  );
}

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](https://neuprint.janelia.org/account).

### NeuprintExecutor Parameters
| Name                  | Description                                             | Type     | 
|-----------------------|---------------------------------------------------------|----------|
| token                 | [neuPrint authentication token](https://neuprint.janelia.org/account)                       | 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.
``` javascript
{
    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.
```bibtex
@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.

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