Clustergrammer JSON Format

The visualization JSON format required for clustergrammer is described here (see example JSON here clustergrammer_example.json). An overview of the format is shown below (note that the group arrays are not shown):

{
  "row_nodes":[
     {
      "name": "ATF7",
      "clust": 67,
      "rank": 66,
      "rankvar": 10,
      "group": []
    }
  ],
  "col_nodes":[
    {
      "name": "Col-0",
      "clust": 4,
      "rank": 10,
      "rankvar": 120,
      "group": []
    }
  ],
  "links":[
    {
      "source": 0,
      "target": 0,
      "value": 0.023
    }
  ]
}

See example workflow or make_clustergrammer.py for examples of how to use the python module to generate a visualization json from a matrix file.

Optional 'views' of the clustergram are encoded in the 'views' value at the base level of the visualization json. These views are used to store filtered versions of the matrix - the links are shared but the views have their own row_nodes/col_nodes. The view attributes are stored in the view object (e.g. N_row_sum).

"views":[
  {
    "N_row_sum": "all",
    "dist": "cos",
    "nodes":{
      "row_nodes": [],
      "col_nodes": []
    }
  }

Views are discussed in more detail the main repo here.

There are three required properties: row_nodes, col_nodes, and links. Each of these properties is an array of objects and these objects are discussed below.

row_nodes and col_nodes properties

required properties: name, clust, rank

row_node and col_node objects are required to have the three properties: name, clust, rank . name specifies the name given to the row or column. clust and rank give the ordering of the row or column in the clustergram.

optional properties: group, value

row_nodes and col_nodes have optional properties: group and value. Group is an array that contains group-membership of the row/column at different dendrogram distance cutoffs. If row_nodes and col_nodes have the property group then a dendrogram will be added the clustergram.

If row_nodes or col_nodes have the property value, then semi-transpaent bars will be made behind the labels that represent this value.

links properties

required properties: source, target, value

Link objects are required to have three properties: source, target, value. source and target give the integer value of the row and column of the tile in the visualization. value specifies the opacity and color of the tile, where positive/negative values result in red/blue tiles (tiles are not made for links with zero value).

optional properties: value_up, value_dn

Links also have the optional properties value_up and value_dn which allow the user to split a tile into up- and down-triangles if a link has both up- and down-values. If a link has only an up- or down-value then a normal square tile is shown.