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:

Calls the "PCA" setup dialog box
Undo (restore the previous scale of the image)
Restore the original (100%) scale of the image
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:


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.


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.


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.


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