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@monicadragan2
monicadragan2 committed Oct 29, 2024
1 parent 83b7c60 commit 0dca4e5
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Showing 2 changed files with 50 additions and 43 deletions.
4 changes: 2 additions & 2 deletions display_tree.js
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Original file line number Diff line number Diff line change
Expand Up @@ -305,7 +305,7 @@ function displayTree(div_id, tree_label, tree_data, target_gene, target_drug, dr
max_genes_in_list = 4
node.on('mousemove', function(d) {
// Compute html info.
if (d.parent && mapSize(d.data.gene_events) != 0) {
if (d.parent) {
html_info = ""
if (d.data.matching_label) {
html_info += "<b>Matching label:</b> " + d.data.matching_label + "<br/>"
Expand All @@ -319,7 +319,7 @@ function displayTree(div_id, tree_label, tree_data, target_gene, target_drug, dr
}
var gene_events = d.data.gene_event_categories
var gene_events_with_details = d.data.gene_event_categories_details
if (gene_events.size) {
if (gene_events) {
html_info += "<p style='margin:6px;'></p><b>Gene events:</b><br/>"
var keys = Array.from(gene_events.keys()).sort().reverse()
for (event of keys) {
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89 changes: 48 additions & 41 deletions oncotreevis.js
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ function oncotreeVIS(data, container_div_id) {
tree = trees[sample_name]["tree"]
matching_labels = new Set(Array.from(getTreeMalignantMatchingLabels(tree).keys()))
for (let matching_label of matching_labels) {
key = matching_label.toString()
key = matching_label
if (key in unique_matching_labels_cohort) {
unique_matching_labels_cohort[key] = false
} else {
Expand Down Expand Up @@ -194,40 +194,46 @@ function oncotreeVIS(data, container_div_id) {

// kNN
knn_json = {}
for (sample_1 in trees) {
tree_1 = trees[sample_1]["tree"]
var matching_labels = new Set(Array.from(getTreeMalignantMatchingLabels(tree_1).keys()))
matching_tree_ids = new Set()
for (let key of matching_labels) {
for (let sample of matching_label_tree_map.get(key)) {
matching_tree_ids.add(sample)
}
}
for (let sample_2 of matching_tree_ids) {
if (sample_1 != sample_2) {
var tree_2 = trees[sample_2]["tree"]
var matching_node_pairs = getMatchingNodes(getTreeNodes(tree_1), getTreeNodes(tree_2))
const [nodes_1, links_1, max_depth_1] = getJSONNodes(sample_1, tree_1)
const [nodes_2, links_2, max_depth_2] = getJSONNodes(sample_2, tree_2)
const max_depth = Math.max(max_depth_1, max_depth_2)
nodes = nodes_1.concat(nodes_2)
links = links_1.concat(links_2)
for (let pair of matching_node_pairs) {
links.push({
"source": sample_1 + "_" + pair[0].data.node_id,
"target": sample_2 + "_" + pair[1].data.node_id,
"similarity": 1,
})
}
knn_json[sample_1 + "_" + sample_2] = {
"sample_1": sample_1,
"sample_2": sample_2,
"nodes": nodes,
"links": links,
"similarity": matching_node_pairs.length,
"max_depth": max_depth
if(mapSize(trees) < 200) {
for (let sample_1 in trees) {
tree_1 = trees[sample_1]["tree"]
//var matching_tree_ids = Object.keys(trees)
var matching_labels = new Set(Array.from(getTreeMalignantMatchingLabels(tree_1).keys()))
matching_tree_ids = new Set()
for (let key of matching_labels) {
for (let sample of matching_label_tree_map.get(key)) {
matching_tree_ids.add(sample)
}
}
}
for (let sample_2 of matching_tree_ids) {
if (sample_1 != sample_2) {
var tree_2 = trees[sample_2]["tree"]
var matching_node_pairs = getMatchingNodes(getTreeNodes(tree_1), getTreeNodes(tree_2))
if (!matching_node_pairs[0]) {
continue
}
const [nodes_1, links_1, max_depth_1] = getJSONNodes(sample_1, tree_1)
const [nodes_2, links_2, max_depth_2] = getJSONNodes(sample_2, tree_2)
const max_depth = Math.max(max_depth_1, max_depth_2)
nodes = nodes_1.concat(nodes_2)
links = links_1.concat(links_2)
for (let pair of matching_node_pairs) {
links.push({
"source": sample_1 + "_" + pair[0].data.node_id,
"target": sample_2 + "_" + pair[1].data.node_id,
"similarity": 1,
})
}
knn_json[sample_1 + "_" + sample_2] = {
"sample_1": sample_1,
"sample_2": sample_2,
"nodes": nodes,
"links": links,
"similarity": matching_node_pairs.length,
"max_depth": max_depth
}
}
}
}
}
data["matching_trees"] = knn_json
Expand Down Expand Up @@ -505,12 +511,12 @@ function populateTreeView(args){
tree_info_div = document.getElementById(tree_info_div_id)
tree_info_div.innerHTML = '<div style="text-align:center;height:100%;display:flex;flex-direction:row;' +
'align-items:center;justify-content:center;"><i>The tree clusters are indicated by<br/>' +
'different background <font color=#A87676>c</font><font color=#E493B3>o</font><font color=#B784B7>l</font><font color=#8E7AB5>o</font>'+
' different background <font color=#A87676>c</font><font color=#E493B3>o</font><font color=#B784B7>l</font><font color=#8E7AB5>o</font>'+
'<font color=#F6995C>r</font><font color=#88AB8E>s</font>. <br/>' +
' Zoom out <i class="fa fa-search-minus"></i> to get the<br/>full overview of the tree clusters.<br/><br/>***<br/><br/>' +
'Click on the trees to visualize<br/>details of each subclone.<br/><br/>' +
'Click on the " <i class="fa fa-desktop fa-sm"></i> show cluster details" icons<br/>' +
'to visualize additional cluster information.'+
' Zoom out <i class="fa fa-search-minus"></i> to get the<br/> full overview of the tree clusters.<br/><br/>***<br/><br/>' +
' Click on the trees to visualize<br/>details of each subclone.<br/><br/>' +
' Click on the " <i class="fa fa-desktop fa-sm"></i> show cluster details" icons<br/>' +
' to visualize additional cluster information.'+
'</i></div>'
tree_info_div.style.backgroundColor = "white"

Expand Down Expand Up @@ -775,7 +781,8 @@ function getTreeNodes(tree_json) {
function getMalignantMatchingLabels(node_list){
var node_map = new Map()
for (node of node_list) {
if (node.data.matching_label && !node.data.is_neutral && mapSize(node.data.gene_states)) {
if ((!node.parent && mapSize(node.data.gene_states)) ||
(node.parent && node.data.matching_label && !node.data.is_neutral)) {
node_map.set(node.data.matching_label, node)
}
}
Expand Down Expand Up @@ -1757,7 +1764,7 @@ function populateHeatmapView(args) {
div_tree_info.style.backgroundColor = "transparent"
div_tree_info.innerHTML = "<div style='text-align:center;height:100%;display:flex;flex-direction:row;" +
"align-items:center;justify-content:center;'><i>Click on the sample names <br/>and" +
" on the colored frames<br/>(corresponding to the given tree clusters)<br/>to visualize additional information.</i></div>"
" on the colored frames<br/>(corresponding to the given tree clusters)<br/> to visualize additional information.</i></div>"

// Data.
data = args.data
Expand Down

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