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example.js
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example.js
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var widgets = require('@jupyter-widgets/base');
var _ = require('underscore');
var d3 = require('d3')
var cgm_fun = require('clustergrammer');
var ini_hzome = require('./hzome_functions');
var Enrichrgram = require('./Enrichrgram');
var url = require("file-loader!./clustergrammer_logo.png");
// version 1.13.1
require('!style!css!./custom.css');
// Custom Model. Custom widgets models must at least provide default values
// for model attributes, including `_model_name`, `_view_name`, `_model_module`
// and `_view_module` when different from the base class.
//
// When serialiazing entire widget state for embedding, only values different from the
// defaults will be specified.
var hello_model = widgets.DOMWidgetModel.extend({
defaults: _.extend({}, widgets.DOMWidgetModel.prototype.defaults, {
_model_name : 'hello_model',
_view_name : 'hello_view',
_model_module : 'clustergrammer_widget',
_view_module : 'clustergrammer_widget',
_model_module_version : '1.13.1',
_view_module_version : '1.13.1',
viz_title : 'default value',
network: ''
})
});
// Custom View. Renders the widget model.
var hello_view = widgets.DOMWidgetView.extend({
render: render_function,
value_changed: function() {
// this.el.textContent = this.model.get('viz_title');
// var inst_network_string = this.model.get('network');
// inst_network = JSON.parse(inst_network_string);
// d3.select(this.el)
// .classed('.widget_viz',true);
}
});
function render_function() {
console.log('\n\n\n working on 7.0.0 migration \n\n\n')
// generate unique id for each visualization
var viz_number = String(Math.round(Math.random()*10000));
var container_name = 'cgm_notebook_' + String(viz_number) ;
if (d3.select('#'+container_name).empty() === false){
var backup_number = String(Math.round(Math.random()*10000));
container_name = container_name + backup_number;
}
// widget-subarea appears to be limited to a width of ~960px in nbviewer
d3.select(this.el)
.append('div')
.classed('clustergrammer_widget', true)
.attr('id', container_name)
.style('width', '975px')
.style('height', '800px');
var inst_network_string = this.model.get('network');
inst_network = JSON.parse(inst_network_string);
var about_string = "<a href='http://clustergrammer.readthedocs.io/clustergrammer_widget.html' target='_blank' ><img src='http://amp.pharm.mssm.edu/clustergrammer/static/img/clustergrammer_logo.png' style='width:130px; margin-left:-5px' alt='clustergrammer'></a>";
var hzome = ini_hzome();
// cgm_model needs to be global
cgm_model = this;
var container_id = '#'+container_name;
// define arguments object
var args = {
root: container_id,
'network_data': inst_network,
'about':about_string,
'row_tip_callback':hzome.gene_info,
'matrix_update_callback':matrix_update_callback,
'cat_update_callback': cat_update_callback,
'sidebar_width':135,
};
setTimeout(make_viz, 10, args);
}
function make_viz(args){
cgm = cgm_fun(args);
check_setup_enrichr(cgm);
console.log('DO NOT UPDATE MATRIX STRING WHEN MAKING VIZ')
}
// hack to prevent matrix update string from running in nbviewer
var inst_url = window.location.href;
var in_nbviewer = false;
if (inst_url.indexOf('nbviewer.jupyter.org') > 0){
in_nbviewer = true;
}
// Enrichrgram specific functions
///////////////////////////////////////////////////////////////
function matrix_update_callback(){
console.log('matrix_update_callback')
if (in_nbviewer === false){
// wait to update matrix string until updating has finished
setTimeout(update_matrix_string, 1500);
}
if (genes_were_found[this.root]){
enr_obj[this.root].clear_enrichr_results();
}
}
function cat_update_callback(){
if (in_nbviewer === false){
setTimeout(update_matrix_string, 1500);
}
}
function update_matrix_string(){
console.log('*** update matrix string')
// update model with matrix string
var inst_mat_string = cgm.export_matrix_string();
cgm_model.model.set("mat_string", inst_mat_string);
cgm_model.touch();
}
var genes_were_found = {};
enr_obj = {};
function check_setup_enrichr(inst_cgm){
var has_enrichrgram = _.has(inst_cgm.params.network_data, 'enrichrgram');
var make_enrichrgram = false;
if (has_enrichrgram){
make_enrichrgram = inst_cgm.params.network_data.enrichrgram;
}
// Toggle Enrichrgram function
if (has_enrichrgram === false){
// check with Hzome whether rows are genes
////////////////////////////////////////////
genes_were_found[inst_cgm.params.root] = false;
var all_rows = inst_cgm.params.network_data.row_nodes_names;
var max_num_genes = 20;
if (all_rows.length > 20){
all_rows = all_rows.slice(0,20);
}
var wait_unit = 500;
var wait_time = 0;
_.each(all_rows, function(inst_name){
setTimeout(check_gene_request, wait_time, inst_cgm, inst_name, run_ini_enrichr);
wait_time = wait_time + wait_unit;
});
} else if (make_enrichrgram) {
// make enrichrgram without checking with Hzome
/////////////////////////////////////////////////
run_ini_enrichr(inst_cgm);
genes_were_found[inst_cgm.params.root] = true;
}
}
function run_ini_enrichr(inst_cgm){
var inst_root = inst_cgm.params.root;
var has_enrichrgram = _.has(inst_cgm.params.network_data, 'enrichrgram');
var make_enrichrgram = false;
if (has_enrichrgram){
make_enrichrgram = inst_cgm.params.network_data.enrichrgram;
}
if (genes_were_found[inst_root] || make_enrichrgram){
if (d3.select(inst_root + ' .enrichr_logo').empty()){
// set up Enrichr category import
enr_obj[inst_root] = Enrichrgram(inst_cgm);
enr_obj[inst_root].enrichr_icon();
// set up Enrichr export in dendro modal
//////////////////////////////////////////
// only display for rows
var enrichr_section = d3.selectAll(inst_root + ' .dendro_info')
.select('.modal-body')
.append('div')
.classed('enrichr_export_section', true)
.style('margin-top', '10px')
// .style('display','none');
enrichr_section
.append('text')
.text('Send genes to ');
enrichr_section
.append('a')
.html('Enrichr')
.on('click', function(){
var group_string = d3.select(inst_root + ' .dendro_text input').attr('value');
// replace all instances of commas with new line
var gene_list = group_string.replace(/, /g, '\n');
///////////////
// clean list
///////////////
var enrichr_info = {list: gene_list, description: 'Clustergrammer gene-cluster list' , popup: true};
// defined globally - will improve
send_to_Enrichr(enrichr_info);
});
}
}
}
function check_gene_request(inst_cgm, gene_symbol, run_ini_enrichr){
if (gene_symbol.indexOf(' ') > 0){
gene_symbol = gene_symbol.split(' ')[0];
} else if (gene_symbol.indexOf('_') > 0){
gene_symbol = gene_symbol.split('_')[0];
}
var base_url = 'https://amp.pharm.mssm.edu/Harmonizome/api/1.0/gene/';
var url = base_url + gene_symbol;
if (genes_were_found[inst_cgm.params.root] === false){
// make sure value is non-numeric
if (isNaN(gene_symbol)){
$.get(url, function(data) {
data = JSON.parse(data);
if (data.name != undefined){
genes_were_found[inst_cgm.params.root] = true;
}
run_ini_enrichr(inst_cgm, gene_symbol);
});
}
}
}
function send_to_Enrichr(options) { // http://amp.pharm.mssm.edu/Enrichr/#help
var defaultOptions = {
description: "",
popup: false
};
if (typeof options.description == 'undefined')
options.description = defaultOptions.description;
if (typeof options.popup == 'undefined')
options.popup = defaultOptions.popup;
if (typeof options.list == 'undefined')
alert('No genes defined.');
var form = document.createElement('form');
form.setAttribute('method', 'post');
form.setAttribute('action', 'https://amp.pharm.mssm.edu/Enrichr/enrich');
if (options.popup)
form.setAttribute('target', '_blank');
form.setAttribute('enctype', 'multipart/form-data');
var listField = document.createElement('input');
listField.setAttribute('type', 'hidden');
listField.setAttribute('name', 'list');
listField.setAttribute('value', options.list);
form.appendChild(listField);
var descField = document.createElement('input');
descField.setAttribute('type', 'hidden');
descField.setAttribute('name', 'description');
descField.setAttribute('value', options.description);
form.appendChild(descField);
document.body.appendChild(form);
form.submit();
document.body.removeChild(form);
}
function abort_request(inst_request){
console.log('ABORTING REQUEST');
inst_request.abort();
}
module.exports = {
hello_model : hello_model,
hello_view : hello_view
};