diff --git a/README.md b/README.md
index 096375e..7febbb9 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,9 @@
# oncotreeVIS – An interactive graphical user interface for visualising mutation tree cohorts
+
+### Web app
+----------
A visualization demo can be seen here: https://cbg-ethz.github.io/oncotreeVIS
@@ -23,47 +26,10 @@
----------
The expected input is a JSON file with the following key values:
-
- The expected input is a JSON file with the following key values:
-
-
-
Key
Data structure
-
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: node_id (string/int, required), matching_label (required),
- size_percent (float, optional), metadata (dictionary, optional), gene_events (dictionary, optional),
- is_neutral (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.
- 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\"}}
- 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).
- 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).
- Example: [{'sample_1': 'AML-73-001', 'sample_2': 'AML-22-001', 'distance': 0.6072}, … ]
-
-
- The JSON files used for the predefined datasets are available on
- github.
-
Load JSON file:
+| Key | Data structure |
+| ----------- | ----------- |
+| clusters|List of lists of tree ids (strings).
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).