The interface

After starting the program the user sees a window that should look similar to figure 3. The display consists of four main windows and additional pop-up displays that can be activated during the analysis. The four windows are as follows:

Figure 3: Screen shot of the main screen of TreeLD

File Window.

This window contains a tree structure with clickable nodes. Clicking on Project summary shows the summary information of the current project and all established tree sets. Clicking on a tree set node loads the selected tree set to the front end. Only one tree set can be loaded at a time.

Map Window.

This window displays the distribution of markers in the region of interest. The spacing of markers in this widow is to scale.

Tree Display.

Here the trees that have been generated by the tree building step of the analysis are displayed. For each focal point, the first generated tree is indicated, with two arrow icons for scrolling to the other trees. Clicking on one of the tree-images opens a new window that shows a full image of the tree. In this image, the phenotypes of the terminal nodes are indicated by a color-scheme.

Analysis Window.

This window displays the LD-evidence that is present in the data. The individual dots show the $\chi^2$ of the individual markers, while the connected line indicates the posterior likelihood for the position of the disease mutation. The window provides four items for further analysis of the data:

Extend tree building

Builds additional trees in a new MCMC, starting at the last tree from the prior Markov chain. See 6.6 for details.

Tree peeling

Starts the analysis of generated trees with treepeeling as described in 6.3.

Import peeling results

Loads saved tree peeling result, re-draw the posterior distribution plot in the front end.

Clear Curve

Clears the posterior distribution curve that is currently displayed.

Clear pointer

Clears the blue triangle pointer that is currently displayed as described in 6.4.

Save Image

Saves current plot as a jpeg file.

The basic control of the program is provided by the menu bar. It helps user to manage the projects, tree sets and analyze the data by providing the following four menus:

File.

This menu provides functionalities to manage projects. Projects are saved on disk with a .tpj extension.

New project

Creates a new project, as described in 6.1.

Open project

Opens an existing project file. It is not possible to have more than one open project at a time.

Close project

Closes current working project, and saves all the changes.

Recent projects

Displays a list of recently visited projects. Open one of the projects by clicking on it.

Exit

Exits the TreeLD program.

View $\rightarrow \chi^2$-plot.

This menu provides utilities to generate a plot of the individual $\chi^2$-values of the markers.

Tree sets.

This menu contains functions to help the user create and manage tree sets. It provides the following functions:

New tree set

Generates a new tree set as described in 6.2.

Remove tree set(s)

Activates a pop-up window for the removal of trees. Click on unwanted tree sets and use the right arrow button move them to the "to be deleted" list.

Generate tree building scripts

Provides the tools to produce scripts to run TreeLD on multiple computers. Refer to 7.2 for detail.

Help.

This menu provides basic help for the use of TreeLD. If you have any questions that neither this function nor the documentation can address, please contact treeldhelp@bsd.uchicago.edu.