The "Tree Diagram" dialog box (Fig. 3.12.1) will open after you set up the tree parameters and create a tree in the "Tree calculation setup" dialog box. In the "Tree diagram" dialog box, the tree is presented as a diagram. If you set the program to build a gene tree, the diagram will display the tree and the expression matrix. If you set the program to build a field tree, the diagram will display only the tree.
Figure 3.12.1 "Tree Diagram" dialog box.
1. Main menu. 2. Toolbar. 3. Diagram view area. 4. Status bar. 5. Ruler. 6. Slider. 7. Shortcut menu.
The "Tree diagram" dialog box has the following elements:
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"Nodes marking mode" - enables the nodes marking mode. This button corresponds to the Edit>Mouse mode>Mark nodes main menu command. |
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"Swap child nodes mode" - enables swapping child nodes. This button corresponds to the Edit>Mouse mode>Swap child nodes main menu command. |
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"Marking of all descent nodes mode" - enables marking all child nodes in the tree. This button corresponds to the Edit>Mouse mode>Marking all descent nodes main menu command. |
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"Unmark all nodes" - unmarks all selections. This button corresponds to the Edit>Mark>Unmark all main menu command. |
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"Options" - calls the "tree options" dialog box. This button corresponds to the Edit>Mark>Options main menu command. |
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"Toggle image" - adds an expression matrix diagram (for a field tree this option in no available). |
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"Open scalable tree" - opens the "Scalable Tree Diagram" dialog box from where you can magnify or reduce the tree obtained. |
The status bar displays information about the expression matrix cell you are pointing to with your mouse button: the gene number, gene name, field number, field name, and the field value.
Use the ruler and the slider to select all leaves located to the left of the vertical line, which appears as you move the slider.
In the "Mark nodes" dialog box (Fig. 3.12.1.1), you can set node selection parameters. To open the dialog box, click Edit>Mark>Mark nodes.
3.13.1.1. The "Mark by leaf name" radio button. If this option is enabled, the nodes are selected by the leaf name specified in the text field below.
3.13.1.2. The "Mark by distance range" radio button. If this option is enabled, the nodes are selected by the specified distance range.
Control buttons:
Figure 3.12.1.1 "Mark nodes" dialog box.
1. Selection of nodes by leaf name. 2. Selection of nodes by distance range. 3. The "OK" button that applies changes and closes the dialog box. 4. The "Cancel" button that cancels changes and closes the dialog box.
In the "Pattern setup" dialog box, you can configure settings for the expression matrix profile. To open the dialog box, click Image>Image setup. See section 3.16.1. about the elements of this dialog box and their functions.
The Options dialog box has the following three tabs:
On the "Colors" tab (Fig. 3.12.2), you can customize colors:
The "Tree background" pane allows you to customize the tree background color:
The "Tree lines" pane allows you to customize the color of tree lines:
The "Tree nodes" pane allows you to customize the color of tree nodes:
The "Guide line" pane allows you to customize the color of the vertical line that appears on the screen as you move the slider:
The "Names background" pane allows you to customize the background color of leaf names:
The "Leaf names" pane allows you to select the font color for leaf names:
The "Selected nodes" pane allows you to select the color of selected nodes:
Figure 3.12.2 "Pattern setup" dialog box. "Colors" tab.
1. "Tree background" pane. 2. "Tree lines" pane. 3. "Tree nodes" pane. 4. "Guide line" pane. 5. "Names background" pane. 6. "Leaf names" pane. 7. "Selected nodes" pane. 8. The "OK" button that applies selected colors and closes the dialog box. 9. The "Apply" button that applies selected colors and leaves the dialog box open. 10. The "Reset to defaults" button that resets defaults colors. 11. The "Cancel" button that cancels selections.
On the "Font & Sizes" tab (Fig. 3.12.3), change the font and size of tree nodes:
In the "Space between leafs" pane, set the distance between leaves.
In the "Nodes radius" pane, change the node radius.
In the "Leaf names" pane, you can change the font for leaf names:
Figure 3.12.3 "Pattern setup" dialog box. "Fonts & Sizes" tab.
1. "Space between leaves" pane. 2. "Nodes radius" pane. 3. The pane for customizing the font for leaf names. 4. The "OK" button that applies selections and closes the dialog box. 5. The "Apply" button that applies selections and leaves the dialog box open. 6. The "Reset to defaults" button that resets default settings. 7. The "Cancel" button that cancels selections.
To open the "Scalable tree diagram" dialog box (Fig. 3.12.1.1):
Figure 3.12.3.1 "Scalable tree diagram" dialog box.
1. Main menu. 2. Toolbar. 3. View and zoom areas.
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"Zoom in vertical" - enlarge the image in vertical direction |
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"Zoom in horizontal" - enlarge the image in horizontal direction |
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"Zoom out vertical" - reduce the image in vertical direction |
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"Zoom out horizontal" - reduce the image in horizontal direction |
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"Zoom 100%" - restore the original size |
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"Zoom min" - set the minimum size |
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"Zoom in" - enlarge the selected area of the image |
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"Zoom out" - reduce the selected area of the image |
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"Go to" - select a node to be displayed on the main diagram |
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"Image creation" - add an expression matrix diagram (for a field tree this button is not available). |