Hierarchical Cluster Assigner

This node takes a hierarchical cluster tree and the same input table that has been used for creating the clustering, and creates an interactive dendrogram using JavaScript. The interactive view allows for the selection of a threshold, which is used to define clusters and assign rows to clusters. In the view, clusters are marked as black dots.

This node is only intended for small data tables (<65,500 rows).

Options

Cluster assignment column name: Sets the name of the assigned cluster column in the output data table.
Assign clusters based on: Select if you want to assign clusters based on a fixed number or based on a distance threshold.
Number of clusters: The number of clusters (i.e. the level in the cluster tree) that should be created.
Distance threshold: The distance below which clusters should be selected.
Use normalized distances for threshold: When checked the value in the "Distance Threshold" field will be interpreted as a normalized distance.

View Configuration

Show warnings in view

If checked, warning messages will be displayed in the view when they occur.

Create image at outport

If checked an SVG image will be created at the outport.

Resize view to fill window

Checking this option resizes the view so that it fills the window.

Width (in px)

The width, in pixels, of the generated SVG image. This is also the width of the view if "Resize view to fill window" is not selected.

Height (in px)

The height, in pixels, of the generated SVG image. This is also the height of the view if "Resize view to fill window" is not selected.

Show threshold bar

If checked, a horizontal line will be displayed at the height of the threshold on the dendrogram.

Enable threshold modification

If checked, the threshold bar can be moved up/down to manually set the threshold.

Chart title (*)

The title shown above the image. If left blank, no title will be shown.

Chart subtitle (*)

The subtitle shown above the image. If left blank, no subtitle will be shown.

Chart Orientation

The orientation of the chart. The following orientations are supported:

Vertical: Standard dendrogram layout with the root node at the top, and the leaves as the bottom of the cart
Horizontal (left): Horizontal dendrogram with the root node on the left and leaves on the right
Horizontal (right): Horizontal dendrogram with the root node on the right and leaves on the left

Enable cluster labels

Displays cluster labels in the view, and enables editing of these labels.

Use log scale for y-axis

Checking this option switches the scaling of the y-axis to logarithmic.

Use cluster colors

If selected, tree leaves will be assigned colors based on their cluster membership.

Use table colors

If selected the leaf colors will be determined by those specified in the input data table.

Select a color palette

The selected color palette will be used to color the clusters in the view.

Interactivity

Enable view edit controls: If checked, all edit controls selected below will be rendered in the view. Unchecking this option disables all edit controls.
Enable title and subtitle editing: Displays a text box to change title or subtitle.
Display full screen button: Displays a button enabling full screen mode.
Enable number of clusters specification: Allows for cluster assignment via number of clusters from the view.
Enable switching y-axis scale: Enables switching between log and linear scaling of the y-axis from within the view.
Enable changing chart orientation: Enables modification of the chart's orientation (i.e. horizontal, vertical, etc.) from within the view.
Enable selection: When this option is checked, data points can be selected in the view. The selection appears in an appended column of the data table.
Show clear selection button: If enabled, a "clear selection" button will be displayed.
Selection column name: Sets the name of the selection column in the output data table.
Publish selection events: Checking this option ensures that other views are notified whenever the selection in the current view is changed.
Subscribe to selection events: Checking this option ensures that this view is notified whenever other views publish new selections.
Enable 'show selected clusters only' option: Enables switching the "show selected clusters only" functionality on/off from within the view.
Show selected clusters only: If checked, only members of the selected clusters will be displayed.
Subscribe to filter events: If checked, the view reacts when applied filters have been changed.
Enable zooming & panning: Enable zooming using the mouse wheel and panning on the view. To start panning click and drag the mouse.
Show zoom reset button: Renders a button to resize the plot to its extent.

Input Ports

: The hierarchical cluster tree that has been created by the Hierarchical Clustering (DistMatrix) node.
: The same data table that has been used to create the clusters.

Output Ports

: An SVG representation of this view.
: The input data table with an appended column denoting cluster assignment.

Popular Predecessors

Popular Successors

Views

Interactive View: Dendrogram: Displays the resulting dendrogram with a bar for selecting the threshold value, which changes the cluster assignments.

Workflows

Developers

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Installation

To use this node in KNIME, install the extension KNIME JavaScript Views (Labs) from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: KNIME AG, Zurich, Switzerland

Plugin version: 5.2.0.v202310301555

On NodePit since: 2023-12-06

Last update: 2024-04-19

KNIME versions: Since v3.7

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