Navigator Nodes are the icons and text that represent the analysis tools or spreadsheet viewers that you are using or have used in your work. Double clicking a Navigator Node causes the associated Viewer window to be displayed. Each Navigator Node is given a default name when it is created, but it can be renamed by right clicking on the Node and selecting Rename Node from the context menu Fig. 3.6 or by single clicking on the Navigator Node’s name.

Navigator Nodes can also be deleted by right clicking on the Node and selecting Delete Node from the popup menu. Note that when deleting a Node, all of the Node’s children will also be deleted, as well as all documentation and notes about those Nodes in the Node Change Log and Edit Annotations windows.

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3.3.1 Viewer Windows

Each data analysis tool is opened in a Viewer window. Spreadsheet Viewers let you view and select data for analysis, while other viewers analyze the data and provide helpful visualizations of data.

Under certain circumstances, Viewer windows automatically generate a duplicate Navigator Node. For example, if a spreadsheet node has a Histogram Node as a child, because the histogram is directly dependent on the state of it’s spreadsheet parent, any change in the state of the spreadsheet causes HelixTree to duplicate the spreadsheet node (but not its children) and make the change in the duplicate leaving the original spreadsheet unchanged. This technique of duplicating parent Navigator Nodes with dependent children helps maintain the integrity of the historical documentation associated with each Navigator Node, making it easier to track changes and produce accurate reports.

There are two types of Viewer windows, a simple viewer and a tabbed viewer. Simple Viewers are associated with a single Navigator Node. Tabbed Viewers are associated with multiple Navigator Nodes. Tabbed Viewers are created for Navigator Nodes that my be duplicated for integrity reasons as described above. For example, by zooming in on a matrix plot a new Navigator Node is created and a tab is added to the bottom of the viewer, titled "Zoom 1". A tabbed viewer has one or more tabs on the bottom of the Viewer that correspond to each of the previously created Navigator Nodes. Clicking on the tabs changes which Navigator Node viewer is displayed. Another example for tabbed viewers occurs when you create ten subset spreadsheets for a given data set, one tabbed viewer is created with ten tabs (a tab for each spreadsheet), and ten Nodes are created in the Project Navigator window. When you double click on one of the ten Spreadsheet Nodes, the tabbed viewer will open with the correct tab selected showing the spreadsheet data for the selected node.

3.3.2 Types of Navigator Nodes and Their Associated Viewers

There is a Navigator Node type for each analysis action that takes place. Except for the Project Node and a Dataset Node, every node can be doubled clicked for its specific Viewer to be displayed. Each type of Navigator Node is described briefly below:

3.3.2.1 The Project Node

The Project Node is the root node that displays the project’s name. The tree of Navigator Nodes descends, either directly or indirectly, from the Project Node. It does not open any Viewer, nor can it be deleted.

3.3.2.2 The Dataset Node

The Dataset Node represents data that has been imported into the project. Its function is to visually identify the data you are analyzing. Every imported data set automatically creates a child Spreadsheet Node. To view a Dataset Node, Double clicking on the child Spreadsheet Node, not the Dataset Node. See chapter 4 , Importing Data, for a complete description of the Dataset Node.

3.3.2.3 The Spreadsheet Node

A Spreadsheet Node represents either all or a subset of a data set. Double clicking on a Spreadsheet Node displays a Spreadsheet Viewer. Using the Spreadsheet Viewer you can select portions of the data set and generate Tree Analysis Nodes for recursive partitioning analysis (see Chapter 7, Interactive Tree Analysis) and for predictions (see Chapter 8, Prediction Recipes). If the Spreadsheet Viewer contains genetic data you will also be able to view plots and tables that will create new Navigator Nodes such as:

• Hardy Weinberg Equilibrium Plot.
• Linkage Disequilibrium Plot.
• Allele Frequency Table.
• Diplotype Table.

Only a spreadsheet view has the ability to export data out of HelixTree. All spreadsheet views have a CSV output option. There is also an option that allows you to export to SAS, EXCEL and most common databases. See Chapter 6, Using the Spreadsheet Viewer, for an explanation of working with a spreadsheet view of the data.

3.3.2.4 Tree Analysis Node

A Tree Analysis Node opens a previously created Tree Viewer when double clicked. The Tree Viewer is the main tool for doing the advanced recursive partitioning analysis provided by HelixTree. See Chapter 7, Interactive Tree Analysis, for a detailed explanation.

3.3.2.5 Multitree Model Node

The Multitree Model Node represents a number of trees that have previously been generated with randomly defined splits. Double clicking a Multitree Node displays a Multitree Viewer. The Multitree Viewer is a powerful analysis tool. It is fully described in Chapter 9, Random Tree Generation. For details on doing predictions with the Multitree Viewer, see Chapter 8, Prediction Recipes. The Multitree Viewer has several outputs that generate child Spreadsheet Nodes:

• View Average Tree Predictions,
• View All Tree Predictions,
• View Usage of Selected Variables, and
• View Frequencies of Selected Variables.

3.3.2.6 Applied Tree Node

The Applied Tree Node represents a list of trees that were created as a result of using a Multitree Model to make predictions on some data. Double clicking on the Applied Tree Node displays an Applied Tree Viewer where you can view the prediction trees. See Chapter 8, Prediction Recipes for details of doing predictions. This Viewer also the same outputs as the Multitree Model Node to generate child Spreadsheet Nodes:

3.3.2.7 Histogram Node

A Histogram Node represents a previously generated histogram. Double clicking on a Histogram Node causes its Histogram Viewer to be displayed. See Chapter 11, Histogram Node Analysis, for a description of the Histogram Viewer.

3.3.2.8 Observation Distance Matrix Node

An Observation Distance Matrix Node represents a previously generated observation distance matrix graph. Double clicking on an Observation Distance Matrix node causes an Observation Distance Matrix Viewer to be displayed. See Chapter 12, Viewing the Observation Distance Matrix for more details.

3.3.2.9 Correlation Interaction Node

The Correlation Interaction Node represents a previously generated correlation interaction graph. Double clicking on a Correlation Interaction Node causes a Correlation Interaction Viewer to be displayed. See Chapter 13, The Correlation Interaction View.

3.3.2.10 Linkage Disequilibrium Node

The Linkage Disequilibrium Node represents a previously generated plot of Linkage Disequilibrium. Double clicking on this node displays the Linkage Disequilibrium Viewer. The Viewer has five outputs that create new Spreadsheet Nodes. Each of these nodes will be a child of the Linkage Disequilibrium Node. See Chapter 14, Linkage Disequilibrium View, for a complete description of this Viewer.

1. Summarize Data For All Points.
2. Output Genotypes for Current Point.
3. Output Genotype Combinations for Current Point.
4. Output Allele Counts for Current Point.
5. Output Allele Combinations for Current Point.
6. Output Carlson Method SNP Tags (for the current X-Axis range of markers)

3.3.2.11 Two-Loci Node

The Two-Loci Node represents a previously generated plot showing the combined effect of two genetic markers. There is one output spreadsheet from this plot that shows split information about the currently selected point on the plot.

3.3.2.12 Hardy Weinberg Equilibrium Node

The Hardy Weinberg Equilibrium Node represents a previously generated Hardy Weinberg Equilibrium Plot. Double clicking on this node displays the Hardy Weinberg Equilibrium Viewer. This Viewer has three outputs that will create other Spreadsheet Nodes as its children. See Chapter 15, Hardy Weinberg Equilibrium View.

1. Summarize All Data.
2. Output All Allele Tables.
3. Output All Genotype Tables.

3.3.2.13 Carlson SNP Tags Node

The Carlson SNP Tags node represents a spreadsheet of SNP tags generated from an LD plot.

3.3.2.14 P Value Node

The P Value Node represents a previously created P Value Plot. Double clicking on this node will display the P Value Plot Viewer.

3.3.2.15 Text Node

The Text Node represents a collection of textual information. Double clicking on this node will open a Text Viewer.

3.3.2.16 Distributed Progress Node

The Distributed Progress Node represents a distributed job which has been moved to the background. Double clicking on this node will cause HelixTree to attempt to reconnect to the distributed server, and display the job status and progress. See 23.4.6.5 for more information on backgrounded jobs.