HierarchicalClusteringViewer (v12) BETA

Introduction

This visualizer provides a tree view (dendrogram) of the results of the HierarchicalClustering module. The dendrogram provides a graphical view of the distance between clusters identified by the algorithm, as well as a heat map of the associated data. This module requires the following files, which are output from the HierarchicalClustering module: 

• A CDT file, which contains the original data, sorted into clusters. 
•  Either a GTR file, which contains the distance measures between gene (row) clusters in the dataset, or an ATR file, which contains the distance measures between sample (column) clusters. When both files are provided, a 2-dimensional "biclustering" of the data is shown. 

Values are displayed in a heat map format, representing higher values in more intense red colors and lower values in more intense blue colors. 

Parameters

* - required

Options

There are a number of options controlling the appearance of the heat map that can be set by clicking the Options button: 

• You can choose between radio buttons for Row Relative and Global color schemes. When the relative choice is selected, the heat map converts values to colors using the mean, minimum, and maximum values in each row. When the global choice is selected the heat map converts values to colors using the mean, minimum, and maximum values in the entire dataset.
• You can choose between the radio buttons Use Color Gradient and Use Discrete Colors. The heat map uses linear color gradient to convert values to colors when the Use Color Gradient button is selected, while a discrete color map is used if the Use Discrete Colors button is selected. A color picker is provided for selecting colors. When specifying discrete colors there is no limit on the number of colors that can added.

Dendrogram Rotation

You can flip a branch in the sample or feature dendrogram by right clicking on the the circle and selecting Flip Dendrogram. 

Note that this feature currently only works on Windows in Firefox or IE11

Add/Edit Labels

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Sample Features This option is currently under development

• To load feature labels, click the Add/Edit labels button and load a GMX file. A complete description of this format is available on the GenePattern website.
• Feature labels use color to annotate features in the heat map
• A color bar appears next to each feature in the feature set in the table.
• Click the Add/Edit labels button and the select Edit>Feature Labels to edit the color or remove the feature set.

Sample Labels

• Sample labels use color to annotate samples in the heat map.
• Create a CLS file. A complete description of this format is available on the GenePattern website.
• A color bar appears below each sample name
• Click the Add/Edit labels button and the select Edit>Feature Labels to edit the color or remove the sample set

Saving Images

Users can save the heat map image to a file by selecting the Save Image button. Supported formats are SVG and PNG. There is the option to save an image of the current view of the heatmap or the entire heatmap. There is a size limit when saving in png format.​ The limit is roughly number of features * number of samples <= 3580000. An error will be displayed if the file is too large to save as PNG.

Find 

To find a feature or sample in the heat map, click the Search button and enter the text and whether to search among the features or the samples and also if the search should be case-insensitive. 

Task Type:
javascript

CPU Type:
any

Operating System:
any

Language:
Java