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Dendrogram

Dendrogram is a package for phylogenetic trees visualization.

Notations​

Now only the Newick tree format is supported.

Viewers​

Dendrogram viewer is a pure typescript component derived from DG.JsViewer to be used as a Datagrok viewer. Exposed properties allow customizing the viewer appearance for the line width and color, the node size and fill color.

Dendrogram properties

The viewer expects a data frame with the tag '.newick' (data frame tree data tag name can be customized with the property 'newickTag') containing tree data, but also allowing to set the 'newick' property for data (the 'newick' property value has higher priority over data frame tag).

//name: Dendrogram
//language: javascript
const csv = await grok.dapi.files.readAsText("System:AppData/Dendrogram/data/tree95df.csv");
const newick = await grok.dapi.files.readAsText("System:AppData/Dendrogram/data/tree95.nwk");
const df = DG.DataFrame.fromCsv(csv);
df.setTag('.newick', newick);
const tv = grok.shell.addTableView(df);
const viewer = await df.plot.fromType('Dendrogram', {});
tv.dockManager.dock(viewer, DG.DOCK_TYPE.RIGHT); // TypeError: Cannot read properties of undefined (reading 'H')

Optimized for large trees​

The Dendrogram viewer is highly optimized to render trees with hundreds of thousands of nodes.

Large tree

File handlers​

Opening file with .nwk, .newick extension will be transformed to a DataFrame of nodes (node, parent, leaf, distance columns) with a DendrogramViewer docked on the right side of the grid. The dendrogram viewer interacts with the data frame on which it is opened on the column with the node names specified in the Node[ColumnName] property. Current state, hover, and selection are supported and displayed with specific styles in the dendrogram and data frame grid.

.nwk file handler with interactivity

Dendrogram injected to grid, hierarchical clustering​

An application developer can inject Dendrogram viewer to a grid linked by row number or leaves' column name. For example Top menu function ML | Hierarchical Clustering calculates the tree on selected features/columns set with specified pairwise distance metric and aggregation method. Mouse over, current, selected and filtered states, row height are synchronized between grid and injected tree in both directions.

ML | Hierarchical Clustering