3.15. "Graph" dialog box
The "Graph" dialog box (Fig. 3.15.1) visualizes the distribution of genes in the space between two main components.
Toolbar buttons and fields:
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Calls the "PCA" setup dialog box |
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Undo (restore the previous scale of the image) |
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Restore the original (100%) scale of the image |
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Redo (restore the undone scale of the image). |
Graph
The graph visualizes the distribution of genes in the space between two main components.
To enlarge the scale of the image, select a rectangle with your left mouse button.
If you select a rectangle with your right mouse button, this will open the "Operations with marked items" dialog box (about this dialog box, see section 3.15.1).
Status bar
The status bar displays:
- The name of the gene you are pointing to with your mouse and the current coordinates of the mouse pointer.

Figure 3.15.1 "Graph" dialog box.
1. Toolbar. 2. Diagram. 3. Status bar.
3.15.1. "Operations with marked items" dialog box
The "Operations with marked items" dialog box (Fig. 3.15.1.1) contains a list of gene names within the selected area and the following control buttons:
<-Select all - selects all genes in the list.
<-Unselect all - unselects all genes in the list.
<-Invert - inverts selection of all genes in the list.
Color - calls the "Color dialog" dialog box from where you can customize colors for the graph and the genes selected in the list.
Profile Graph - calls the "Profile graph" dialog box that visualizes the expression profiles of genes selected in the list (profiles are drawn by fields, which were taken into account in the PCA computations).
Gene Selection - creates a table containing the genes selected in the list.
Tree - calls the "Tree calculation setup" dialog box from where you can build a tree of the genes selected in the list.
Cancel - quits the dialog box.
When you click the "Profile Graph", "Gene Selection", and "Tree" buttons, the program will create new tables containing genes that were subjected to these computations.

Figure 3.15.1.1 "Operations with marked items" dialog box.
1. List of genes within the selection area. 2. The "Select all" button that selects all genes in the list. 3. The "Unselect all" button that unselects all genes in the list. 4. The "Invert" button that inverts selections. 5. The button that calls the "Color" dialog box. 6. The button that calls the "Profile graph" dialog box. 7. The button that creates a new table. 8. The button that calls the "Tree calculation setup" dialog box. 9. The "Cancel" button that closes the dialog box.
3.15.2. "PCA" dialog box
In the "PCA" dialog box, you can change graphics settings for the "Graph" dialog box. To access the "PCA" dialog box, click the
toolbar button. The "PCA" dialog box has three tabs: "Axis", "Ticks", and "Panel".
"Axis" tab
On the "Axis" tab (Fig. 3.15.2.1), configure the graphics options for axes.
- In the "Bottom title" pane, set the parameters for the bottom axis title:
- Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a font for the title.
- The "Old font" pane shows old font settings.
- The "New font" pane displays new font settings.
- Check/uncheck the "Visible" checkbox to display/hide the axis name.
- In the "Bottom labels" pane, set the parameters for bottom axis labels:
- Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a font.
- The "Old font" pane shows old font settings.
- The "New font" pane displays new font settings.
- Check/uncheck the "Visible" checkbox to display/hide the axis labels.
- In the "Left title" pane, configure settings for the left axis title:
- Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a font.
- The "Old font" pane shows old font settings.
- The "New font" pane displays new font settings.
- Check/uncheck the "Visible" checkbox to display/hide the axis title.
- In the "Left labels" pane, configure settings for the left axis labels:
- Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a font.
- The "Old font" pane shows old font settings.
- The "New font" pane displays new font settings.
- Check/uncheck the "Visible" checkbox to display/hide the axis labels.
- In the "Left" pane, set the minimum and maximum values for the left axis:
- The "AutoMin" checkbox. If the checkbox is checked, the minimum value will be set automatically. If the checkbox is unchecked, you can type the desired minimum value in the "Min" field.
- The "AutoMax" checkbox. If the checkbox is checked, the maximum value will be set automatically. If the checkbox is unchecked, you can type the desired maximum value in the "Max" field.
- In the "Bottom" pane, set the minimum and maximum values for the bottom axis:
- The "AutoMin" checkbox. If the checkbox is checked, the minimum value will be set automatically. If the checkbox is unchecked, you can type the desired minimum value in the "Min" field.
- The "AutoMax" checkbox. If the checkbox is checked, the maximum value will be set automatically. If the checkbox is unchecked, you can type the desired maximum value in the "Max" field.
- In the pane below, you can edit the titles of the axes:
- In the "Bottom title" field, edit the title of the bottom axis.
- In the "Left title" field, edit the title of the left axis.

Figure 3.15.2.1 "PCA" dialog box. "Axis" tab.
1. The pane for changing settings for the bottom axis title. 2. The pane for changing settings for the bottom axis labels. 3. The pane for changing settings for the left axis title. 4. The pane for changing settings for the bottom axis labels. 5. The pane for adjusting the minimum and maximum values for the bottom axis. 6. The pane for adjusting the minimum and maximum values for the left axis. 7. The field for editing the titles of the axes. 8. The "Apply" button that applies changes and leaves the dialog box open. 9. The "OK" button that closes the dialog box and applies changes. 10. The "Cancel" button that closes the dialog box and cancels changes.
"Ticks" tab
On the "Ticks" tab (Fig. 3.15.2.2), you can customize graphics options for axis ticks.
- In the "Bottom ticks" pane, customize the major ticks on the bottom axis:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change color for the ticks.
- The "Old color" pane shows the old color of ticks.
- The "New color" pane shows the new color of ticks.
- Check/uncheck the "Visible" checkbox to show/hide ticks.
- The "Length" field specifies the space between ticks.
- The "Increm." field specifies the increment.
- In the "Bottom minor ticks" pane, customize the minor ticks on the bottom axis:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change color for the ticks.
- The "Old color" pane shows the old color of ticks.
- The "New color" pane shows the new color of ticks.
- Check/uncheck the "Visible" checkbox to show/hide ticks.
- The "Length" field specifies the space between ticks.
- The "Count." field specifies the number of minor ticks between the major ones.
- In the "Left ticks" pane, customize the major ticks on the left axis:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change color for the ticks.
- The "Old color" pane shows the old color of ticks.
- The "New color" pane shows the new color of ticks.
- Check/uncheck the "Visible" checkbox to show/hide ticks.
- The "Length" field specifies the space between ticks.
- The "Increm." field specifies the increment.
- In the "Left minor ticks" pane, customize the minor ticks on the left axis:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change color for the ticks.
- The "Old color" pane shows the old color of ticks.
- The "New color" pane shows the new color of ticks.
- Check/uncheck the "Visible" checkbox to show/hide ticks.
- The "Length" field specifies the space between ticks.
- The "Count." field specifies the number of minor ticks between the major ones.

Figure 3.15.2.2 "PCA" dialog box. "Ticks" tab.
1. The "Bottom ticks" pane. 2. The "Bottom minor ticks" pane. 3. The "Left ticks" pane. 4. The "Left minor ticks" pane. 5. The "Apply" button that applies changes and leaves the dialog box open. 6. The "OK" button that applies changes and closes the dialog box. 7. The "Cancel" button that cancels changes and closes the dialog box.
"Panel" tab
On the "Panel" tab (Fig. 3.15.2.3), you can select the background color for the graph and graph area.
- In the "Frame" pane, you can select the background color for the graph area:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change the background color.
- The "Old color" pane shows the old color.
- The "New color" pane shows the new color.
- In the "Background" pane, you can select the background color for the graph:
- The "Color" button calls the "Select color" dialog box (see section 3.18), from where you can change the background color.
- The "Old color" pane shows the old color.
- The "New color" pane shows the new color.

Figure 3.15.2.3 "PCA" dialog box. "Panel" tab.
1. The "Frame" pane for selecting the background color for the graph area. 2. The "Background" pane for selecting the background color for the graph. 3. The "Apply" button that applies changes and leaves the dialog box open. 4. The "OK" button that applies changes and closes the dialog box. 5. The "Cancel" button that cancels changes and closes the dialog box.
Control buttons
- Apply - applies changes and leaves the dialog box open
- OK - applies changes and closes the dialog box
- Cancel - cancels changes and closes the dialog box