Published
Edited
Apr 2, 2022
2 forks
filtered_tox21_cells_targets = reshaped_tox21_datasets_for_all_compounds
.filter(item => selected_cell_types.includes(item["Cell type"]))
.filter(item => selected_target_types.includes(item["Target type"]))
.filter(item => selected_target_families.includes(item["Target family"]))
target_families = Array.from(new Set(reshaped_tox21_datasets_for_all_compounds.map(item => item["Target family"])))
target_types = Array.from(new Set(reshaped_tox21_datasets_for_all_compounds.map(item => item["Target type"])))
cell_types = cell_types_with_null.filter(item => item != null).sort()
cell_types_with_null = Array.from(new Set(reshaped_tox21_datasets_for_all_compounds.map(item => item["Cell type"])))
reshaped_tggates_fold_changes = [].concat(...tggates_significant_fold_changes)
reshaped_drugmatrix_fold_changes = [].concat(...drugmatrix_significant_fold_changes)
tggates_significant_fold_changes.forEach((dataset, index_dataset) => get_fold_changes_with_samplenames(dataset, index_dataset, tggates_samples_array))
drugmatrix_significant_fold_changes.forEach((dataset, index_dataset) => get_fold_changes_with_samplenames(dataset, index_dataset, drugmatrix_samples_array))
get_fold_changes_with_samplenames = function(dataset, index_dataset, array_of_samplenames) {
dataset.forEach((row, index_row) => {
row["Sample"] = array_of_samplenames[index_dataset]
return row
})
return dataset
}
tggates_significant_fold_changes = get_datasets_from_promises(tggates_promised_fold_changes)
drugmatrix_significant_fold_changes = get_datasets_from_promises(drugmatrix_promised_fold_changes)
get_datasets_from_promises = function(array_of_promises) {
return Promise.all(array_of_promises).then(item => item.map(dataset => dataset.results.map(row => row.data)))
}
get_unique_sample_names = function(array_of_datasets, selected_datasets) {
var samplenames = [];
selected_datasets.forEach(dataset_id =>
{var samplename = array_of_datasets.filter(object => object["Dataset ID"] == dataset_id)[0]["Sample"]
samplenames.push(samplename)}
)
return samplenames;
}
tggates_samples_array = get_unique_sample_names(tggates_datasets_of_selected_compound, unique_tggates_fold_changes_datasets)
drugmatrix_samples_array = get_unique_sample_names(drugmatrix_datasets_of_selected_compound, unique_drugmatrix_fold_changes_datasets)
tggates_promised_fold_changes = get_promised_fold_changes_datasets(unique_tggates_fold_changes_datasets)
drugmatrix_promised_fold_changes = get_promised_fold_changes_datasets(unique_drugmatrix_fold_changes_datasets)
get_promised_fold_changes_datasets = function(array_of_datasets) {
return array_of_datasets.map(dataset => {
return fetch(base_url_edelweiss + dataset + "/versions/latest/data", query_options_for_fold_changes).then(response_dataset => {
if (!response_dataset.ok) throw new Error(response_dataset.status);
return response_dataset.json();
})
})
}
query_options_for_tox21 = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
exactSearch: [{column: ["DTXSID"]}, compound_dtxsid]
},
columns: ["DTXSID"]
})
}
}
query_options_for_fold_changes = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
or: [
{lt: [{column: ["logFC"]}, -logfc_threshold]},
{gt: [{column: ["logFC"]}, logfc_threshold]},
]
},
columns: ["logFC", "SYMBOL", "ENSEMBL", "ENTREZID"]
})
}
}
unique_tggates_fold_changes_datasets = get_unique_fold_changes_datasets(tggates_datasets_of_selected_compound)
unique_drugmatrix_fold_changes_datasets = get_unique_fold_changes_datasets(drugmatrix_datasets_of_selected_compound)
function get_unique_fold_changes_datasets(array_of_datasets) {
var set_of_datasets = new Set(array_of_datasets.map(x =>x["Dataset ID"]));
return Array.from(set_of_datasets).filter(function(item) {return item != null;})
}
reshaped_tox21_datasets_for_all_compounds = reshape_tox21_datasets_for_all_compounds(tox21_datasets_of_selected_compound_with_samplename)
reshape_tox21_datasets_for_all_compounds = function(array_of_datasets) {
var j;
var hitcall;
var ic50;
const unique_compound_datasets = Array.from(new Set(array_of_datasets.map(item => item["Summary data"])));
var results = [];
// loop over unique compound datasets and evaluate
for (j = 0; j < unique_compound_datasets.length; j++) {
const dataset_id = unique_compound_datasets[j];
const datasets = array_of_datasets.filter(item => item["Summary data"] == dataset_id);
const hitcalls = datasets.map(item => item["Hit call"]);
const unique_hitcalls = Array.from(new Set(hitcalls));
const ic50_values = datasets.map(item => item["IC50"]);
if (unique_hitcalls.length > 1) {
hitcall = "ambiguous";
} else {
hitcall = unique_hitcalls[0];
};
if (hitcall == "active") {
const arrSum = ic50_values => ic50_values.reduce((a,b) => a + b, 0);
ic50 = arrSum / ic50_values.length;
} else {
ic50 = null;
}
const dataset_object = datasets[0];
results.push({
"Hit call": hitcall,
"Organism": dataset_object["Organism"],
"Cell type": dataset_object["Cell type"],
"Design type": dataset_object["Design type"],
"Target type": dataset_object["Target type"],
"Target family": dataset_object["Target family"],
"Biological process": dataset_object["Biological process"],
"Sample": dataset_object["Sample"],
"IC50": ic50,
});
};
return results;
}
tox21_datasets_of_selected_compound_with_samplename = tox21_datasets_of_selected_compound.map(function(obj) {
obj["Sample"] = obj["Dataset name"].replace("EPA-InVitroDBV3.2-TOX21_", "").replace("_", " ");
return obj;
})
tggates_datasets_of_selected_compound_with_samplename = tggates_datasets_of_selected_compound.map(function(obj) {
obj["Sample"] = obj["Organism"] + " / " + obj["Study type"] + " / " + obj["Organ"] + " / " + obj["Dosing"] + " / " + obj["Dose"] + " / " + obj["Duration"] + " " + obj["Duration unit"];
return obj;
})
tox21_datasets_of_selected_compound = fetch_dataset_to_array(tox21_summary_url, query_options_filter_inchikey_lowercase)
tggates_datasets_of_selected_compound = fetch_dataset_to_array(tggates_summary_url, query_options_filter_inchikey)
drugmatrix_datasets_of_selected_compound = fetch_dataset_to_array(drugmatrix_summary_url, query_options_filter_compound)
query_options_filter_inchikey_lowercase = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
exactSearch: [{ column: ["InChI key"] }, selected_compound_inchikey.replace('InChIKey=','')],
}
})
}
}
query_options_filter_inchikey = {
return {
method: 'POST',
body: JSON.stringify({
condition: {exactSearch: [{ column: ["InChI Key"] }, selected_compound_inchikey]}
})
}
}
query_options_filter_compound = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
exactSearch: [{ column: ["Compound"] }, selected_compound]
}
})
}
}
selected_compound_smiles = selected_compound_object["SMILES"]["canonical"]
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());
}
compound_svg = get_svg_from_smiles(selected_compound_smiles)
selected_compound_inchikey = selected_compound_object["InChI Key"]
selected_compound_object = drugmatrix_summary_dataset.find(obj => {return obj.Compound === selected_compound})
compound_options = Array.from(new Set(drugmatrix_summary_dataset.map(obj => obj.Compound))).sort()
drugmatrix_summary_dataset = fetch_dataset_to_array(drugmatrix_summary_url, query_options_for_summary_compounds)
query_options_for_summary_compounds = {
return {
method: 'POST',
body: JSON.stringify({
columns: ["Compound", "SMILES", "InChI Key", "InChI", "CAS", "IUPAC name"]
})
}
}
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));
}
tox21_summary_url = base_url_edelweiss + tox21_summary_id + "/versions/latest/data"
tggates_summary_url = base_url_edelweiss + tggates_summary_id + "/versions/latest/data"
drugmatrix_summary_url = base_url_edelweiss + drugmatrix_summary_id + "/versions/latest/data"
drugmatrix_summary_id = '9c1c25e0-2943-4c36-9123-ccbb1f4ef2ae'
tggates_summary_id = '16a4418e-01ff-4dcd-9b2d-90ef00565655'
tox21_summary_id = "8cc0534a-5e52-4253-a736-40f616b84a41"
base_url_edelweiss = 'https://api.kit.edelweissconnect.com/datasets/'
import {Select, Range, Toggle} from "@observablehq/inputs"
import {select, slider} from "@jashkenas/inputs"
import {vl} from "@vega/vega-lite-api"
import {render_data_table, table_styles, displayImage, displayCaution} from '@info474/utilities'
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