pathways = enrichr_output['KEGG_2015'].map(item => {return {
Pathway: item[1],
'Gene symbol': item[5].join(', '),
Rank: item[0],
'p-value': item[2],
'Adj. p-value': item[6],
'Z-score': item[3],
'Combined score': item[4]
}})
enrichr_output = fetch_enrichr(enrich_get_url, {method: 'GET'})
enrich_get_url = fetch_enrichr("https://amp.pharm.mssm.edu/Enrichr/addList", enrichr_post_query_options)
.then(content => content.userListId)
.then(userid => "https://amp.pharm.mssm.edu/Enrichr/enrich?userListId=" + userid + "&backgroundType=KEGG_2015")
formData = {
var f = new FormData()
f.append('list', genes_for_lineplot.join('\n'))
return f}
enrichr_post_query_options = {
return {
method: "POST",
body: formData}
}
function fetch_enrichr(url, query_options) {
return fetch(url, query_options).then(response_dataset => {
if (!response_dataset.ok) throw new Error(response_dataset.status);
return response_dataset.json();})
}
unique_deregulated_genes = Array.from(new Set(deregulated_genes))
deregulated_genes = [].concat(...reshaped_tggates_fold_changes).map(item => item.SYMBOL)
reshaped_tggates_fold_changes = [].concat(...tggates_significant_fold_changes)
tggates_significant_fold_changes.forEach((dataset, index_dataset) => get_fold_changes_with_samplenames(dataset, index_dataset, tggates_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)
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)
tggates_promised_fold_changes = get_promised_fold_changes_datasets(unique_tggates_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_fold_changes = {
return {
method: 'POST',
body: JSON.stringify({
condition: {
and: [
{lt: [{column: ["adj.P.Val"]}, padj_threshold]},
{or: [
{lt: [{column: ["logFC"]}, -logfc_threshold]},
{gt: [{column: ["logFC"]}, logfc_threshold]},
]},
]
},
columns: ["logFC", "SYMBOL", "ENSEMBL", "ENTREZID", "adj.P.Val"]
})
}
}
unique_tggates_fold_changes_datasets = get_unique_fold_changes_datasets(tggates_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;})
}
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;
})
tggates_datasets_of_selected_compound = fetch_dataset_to_array(tggates_summary_url, query_options_filter_inchikey)
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 = tggates_summary_dataset.find(obj => {return obj.Compound === selected_compound})
compound_options = Array.from(new Set(tggates_summary_dataset.map(obj => obj.Compound))).sort()
tggates_summary_dataset = fetch_dataset_to_array(tggates_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));
}
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'
base_url_edelweiss = 'https://api.kit.edelweissconnect.com/datasets/'
import {Select, Range, Toggle, Table} 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'
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.
