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README.md

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 ### Web app
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 <b>A visualization demo can be seen here:</b> https://cbg-ethz.github.io/oncotreeVIS
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 ### Abstract
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@@ -28,8 +28,10 @@ The expected input is a JSON file with the following key values:<br/><br/>
 
 | Key      | Data structure |
 | ----------- | ----------- |
-| clusters|List of lists of tree ids (strings).<br/><br/>Example:[['AML-55-001', 'AML-33-001', 'AML-57-001', 'AML-11-001'],  ['AML-77-001'], ['AML-50-001', 'AML-102-001'], … ] |
+| trees | Nested data structure representing a tree in JSON format, as used in D3.js and anytree (python) libraries. Each node has one or more child nodes (node.children), except for the leaves. In addition, each node has the following attributes: <i>node_id</i> (string/int, required), <i>matching_label</i> (required), <i>size_percent</i> (float, optional), <i>metadata</i> (dictionary, optional), <i>gene_events</i> (dictionary, optional), <i>is_neutral</i> (boolean, optional). The gene_events attribute has two predefined keys (“mutation” and “CNA”), but any other key names can be used. The values for the “CNA” event key are specifically interpreted as amplification or deletion amounts w.r.t. the neutral states. The first three letters of the event key are used in the visualization for displaying a summary for the gene events. <br/><br/>Example of JSON tree: "AML-03-001": {"tree": {"node_id": 0, "matching_label": 0, "children": [{"node_id": 407, "matching_label": 14, "size_percent": 0.228, "gene_events": {"FLT3-ITD": {"mutation": ""}}, "children": [{"node_id": 408, "matching_label": 5, "size_percent": 0.772, "gene_events": {"NPM1": {"mutation": "p.L287fs"}}}]}]}, "metadata": {"Chemo": "No", "Gender": "Female", "VitalStatus": "Dead NOS", "age": 59, "Diagnosis": "AML", "Response": "CR"}}<br/><br/>Examples for gene_events dictionary: "gene_events": {"NPM1": {"mutation": "p.L287fs"}, "AKT3": {"CNA": 2}, "JAK2": {"CNA": -1}, "TP53": {"CNA”: "-", “expression”: “0.34”}}|
+| clusters|List of lists of tree ids (strings).<br/><br/>Example: [['AML-55-001', 'AML-33-001', 'AML-57-001', 'AML-11-001'],  ['AML-77-001'], ['AML-50-001', 'AML-102-001'], … ] |
 | pairwise_distances   | List of dictionaries where the keys are the tree ids of the pair of trees (strings) and the distance score (float).<br/><br/> Example: [{'sample_1': 'AML-73-001', 'sample_2': 'AML-22-001', 'distance': 0.6072}, … ]|
+| highlighted_genes | Styles used: “bold”, “italic”, color code.<br/><br/>Example: {“bold”: [“JAK2”, “PTEN”, “TP53”, “AKT1”]} |
 
 <br/><br/>The JSON files used for the predefined datasets are available in the <i>data</i> folder.