Clustering Analysis

This operation performs a Clustering Analysis on Aligned Peak Lists.

Usage

You can execute this operation by clicking the button or following the menu Analysis/Clustering Analysis.

A dialog will appear allowing you to select the following options:

• Data: Labeled Aligned Peak List Set or Unlabeled Peak List.
• Minimum variance: peaks with a variance lower or equals to this value are removed.
• Peak list: if provided, only these peaks will be analyzed.
• Cluster Reference Value: which value use when comparing two clusters.
• Distance Function: function used to measure the distance between to clusters.
• Conversion Values: presence, percentage of presence or intensity.
• Intra-sample Minimum Presence: when using the percentage of presence, a value between 0 and 100 indicating the minimum percentage of presence of a peak to be considered.
• Deep Clustering: check if you want to perform a spectrum-based clustering instead of sample-based.
• Output directory: optionally, a directory to store the clustering results. If it is not provided, a temporary directory will be used.

Output and visualization

As a result of this operation, a new Clustering is added to the clipboard. Every time a new Clustering Result is accessible, it can be inspected with the Cluster Explorer View.

Export results

The files generated by this analysis that are stored in the chosen Output directory can be opened using JTreeViewer (http://jtreeview.sourceforge.net/).

In addition, you can export the hierarchical clustering using the "Export" menu. This menu offers you the following options:

• Export to Postscript: exports the entire hierarchical clustering into a Postscript file. Note that if you have selected an specific area of the heatmap, this will be the exported area.
• Export to Image: exports the entire hierarchical clustering into a PNG/JPG image file. Note that if you have selected an specific area of the heatmap, this will be the exported area.
• Export ColorBar to Postscript: exports the color bar used in the heatmap into a Postscript file.
• Export ColorBar to Image: exports the color bar used in the heatmap into a PNG/JPG file.
• Save Tree Image: exports the peaks tree into a PNG/JPG file.
• Save Thumbnail Image: exports the heatmap into a PNG/JPG file.
• Save Zoomed Image: exports the zoomed heatmap into a PNG/JPG file.
• Export as CSV: exports the heat map matrix into a CSV file.