Overlay nodes (deprecated)

This API is deprecated so use the Place new nodes instead of this.

https://hexcalc.ucsc.edu/query/overlayNodes

HTTP POST with content-type: application/json

data-type: json

Note that this api is deprecated and Place Nodes should be used instead.

This API takes data for one or more of your nodes and places them over the background nodes of an existing map.

Content Example

{
   "map": "CKCC/v1",
   "layout": "mRNA",
   "email": [
       "mok66@gmail.com",
       ...
   ],
   "viewServer": 'https://tumormap.ucsc.edu',
   "individualViewUrls": true,
   "neighborCount": 8,
   "nodes": {
       "MySample1": {
           "ALK": 0.897645,
           "TP53": 0.904140,
           ...
       },
       "MySample2": {
           "ALK": 0.897645,
           "TP53": 0.904140,
           ...
       },
       ...
   }
}

Where:

  • map : a unique identifier. If the map belongs to a map group, that is included before the specific map separated by a slash as in the example.
  • layout : name of a particular layout of nodes within a map
  • email : optional; one or more email addresses to receive the response
  • viewServer : optional; defaults to https://tumormap.ucsc.edu; the URL to view the results
  • individualViewUrls : optional; defaults to False; True means a view URL for each node will be returned; False means all node positions will be returned in one view URL
  • neighborCount : optional; defaults to 6; number of nearest neighbors to consider in placing each node
  • nodes : contains a nodes object of node objects with feature names and values as properties of each node

Response success

This is returned as HTTP 200 with the content as a JSON string in the form:

{
   "nodes": {
       "MySample1": {
           "url": "https://tumormap.ucsc.edu/?bookmark=55631067a",
           "neighbors": {
                   "node1": 0.352,
                   "node2": 0.742,
                   ...
               }
           }
       },
       "MySample2": {
           "url": "https://tumormap.ucsc.edu/?bookmark=55631067a",
           "neighbors": {
               "node1": 0.275,
               "node2": 0.965,
               ...
           }
       },
       ...
   }
}

Where:

  • nodes : contains the scores of the most similar neighbor nodes for each placed node.
  • url: view the new nodes overlaying the map with this for each node:
    • a marker pointing out the node
    • a new attribute of ‘<requested-node>: neighbors’ that shows the nearest neighbors in yellow
    • a new attribute of ‘<requested-node>: neighbor values’ that shows the similarity score for each neighbor
  • neighbors : contains the scores of the most similar neighbors.

Note that if the optional input parameter of ‘individualViewUrls’ is true, only one node will be at each URL. Otherwise the URLs returned for each node will be identical and contain all nodes.

Response error

Response errors have some HTTP code other than 200, with JSON content that may contain a stack trace, such as:

{
   "error": "Some message."
   "stackTrace" "an optional stack trace"
}