Public
Edited
Oct 19, 2022
customDomain = ['Inactive', 'Not tested', -12, -11, -10, -9, -8, -7, -6, -5, -4, -3]
customColors = ['white', '#c4c4c4', '#f56c3f', '#f58a3f', '#f4a946', '#f6c659', '#f6e072', '#d8e17e', '#bddf93', '#b8e2b3', '#caebd7', '#c4ddd1']
array_compounds = get_unique_elements(dataset, "Compound")
array_assays = ["PC10 AR", "PC10 Era", "PC20 AR-anti", "PC20 ERa-anti"]
array_svg = Promise.all(array_smiles.map(smiles => function_get_svg_from_smiles(smiles.canonical)))
numeric_dataset = clean_to_numeric_dataset()
parseEndpointValue = function(val) {
// check if value is null, then compound was not tested
if (val == null) {
return "Not tested"
} else if (val.startsWith(">")) {
// check if compound is inactive
return "Inactive"
} else {
// otherwise compound was active and return a number
return parseInt(val)
}
}
clean_to_numeric_dataset = function() {
var arr = [];
var i;
for (i = 0; i < dataset.length; i++) {
var obj = dataset[i]
arr.push({
'Compound': obj['Compound'],
'Endpoint': 'PC10 AR',
'Value': parseEndpointValue(obj['PC10 AR']),
'Original value': obj['PC10 AR']
})
arr.push(
{'Compound': obj['Compound'],
'Endpoint': 'PC10 Era',
'Value': parseEndpointValue(obj['PC10 Era']),
'Original value': obj['PC10 Era']
})
arr.push({
'Compound': obj['Compound'],
'Endpoint': 'PC20 AR-anti',
'Value': parseEndpointValue(obj['PC20 AR-anti']),
'Original value': obj['PC20 AR-anti']
})
arr.push({
'Compound': obj['Compound'],
'Endpoint': 'PC20 ERa-anti',
'Value': parseEndpointValue(obj['PC20 ERa-anti']),
'Original value': obj['PC20 ERa-anti']
})
}
return arr
}
clean_dataset= dataset.map(item => { return {
'Compound': item['Compound'],
'Molecular formula': item['Molecular formula'],
'PC10 AR': parseFloat(item['PC10 AR']).toFixed(2),
'PC10 Era': parseFloat(item['PC10 Era']).toFixed(2),
'PC20 AR-anti': parseFloat(item['PC20 AR-anti']).toFixed(2),
'PC20 ERa-anti': parseFloat(item['PC20 ERa-anti']).toFixed(2),
'Similarity': item['SMILES (Canonical)']['similarity'].toFixed(2)
}
})
targetSmiles = {
if (selectedCompound.value == null) {
return smiles
} else {
return selectedCompound.value['SMILES (Canonical)']['canonical']
}
}
query_options = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
gt: [{tanimotoSimilarity: [targetSmiles, { column: ["SMILES (Canonical)"] }]}, tanimoto_threshold]
},
orderBy: [
{expression: {tanimotoSimilarity: [targetSmiles, { column: ["SMILES (Canonical)"] }]}, ordering: "descending"}
]
})
}
}
function_get_svg_from_smiles = function get_svg_from_smiles(smiles) {
const safeSmiles = encodeURIComponent(smiles);
const svg_url = "https://chemidconvert.cloud.douglasconnect.com/v1/asSvg?width=200&height=200&smiles=" + safeSmiles;
return fetch(svg_url).then(response => response.text());
}
array_smiles = get_unique_elements(dataset, "SMILES (Canonical)")
get_unique_elements = function(array, parameter) {
return Array.from(new Set(array.map(item => item[parameter])))
}
dataset = fetch_dataset_to_array(dataset_url, query_options)
full_array_compounds = get_unique_elements(full_dataset, "Compound")
full_array_cas = get_unique_elements(full_dataset, "CAS")
full_dataset = fetch_dataset_to_array(dataset_url, {})
function fetch_dataset_to_array(dataset_url, query_options) {
return fetch(dataset_url, query_options).then(response_dataset => {
if (!response_dataset.ok) throw new Error(response_dataset.status);
return response_dataset.json();}).then(json => json.results.map(x => x.data));
}
dataset_url = base_url_edelweiss + dataset_id + "/versions/latest/data"
dataset_id = "c2603d1f-9d3a-4d91-96aa-10ce675d2b6b"
base_url_edelweiss = 'https://api.edelweissdata.com/datasets/'
// Import libraries for data table rendering
import {render_data_table} from '@info474/utilities'
import {select, textarea, text, slider} from "@jashkenas/inputs"
import {Select, Range, Toggle, Table} from "@observablehq/inputs"
import {vl} from "@vega/vega-lite-api"
Purpose-built for displays of data
Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
