Principal components

Calculating and visualizing the main components can be completed using the Calculate>Principal Component Analysis commands' group of the main menu.

Calculating the components.
The Calculate>Principal Component Analysis>Calculate command is purposed for calculating the principal components. During the calculations appears the information windows, which disappears on calculations are finished.

Visualizing the main components.

The application provides the possibility to visualize the principal components of sequences and aminoacidic residues both in 2D and 3D space. Plots can be opened with use of the following commands of the application's main menu:
• PCA 2D proteins - opens the "Protein PCA Diagram 2D" window showing the 2D plot of the sequence's main components.
• PCA 3D proteins - opens the "Protein PCA Diagram 3D" window showing the 3D plot of the sequence's main components.
• PCA 2D residues - opens the "Residue PCA Diagram 2D" window showing the 2D plot of the residues' main components.
• PCA 3D residues - opens the "Residue PCA Diagram 3D" (see 1) window showing the 3D plot of the residues' main components.

The composition and functions of these four windows are similar.

Figure 1.

The control panel contains:

• The button returns the plot in the originally loaded position.
• The button scales the image into the plot's visualization area (for 3D plots only).
• The button switches selection mode on.
• The X axis list allows selecting the X axis components.
• The Y axis list allows selecting the Y axis components.
• The Z axis list allows selecting the Z axis components (for 3D plots only).

The plot visualization area allows:
Zooming image in and out. To perform this operation use the mouse pointer while the "Shift" button is pressed. Moving the pointer up zooms the image out, moving it down zooms the image in.
Moving the image. To perform this operation use the mouse pointer while the "Ctrl" button is pressed.
Rotating the image (for 3D plots only). To perform this operation use the mouse pointer.
Selection is to be made by the mouse left button. Selection mode runs on by the button. Identifiers of sequences selected in the plot area are automatically selected in the sequences area of the main window and vice versa. Aminoacidic residues selected in the plot area are automatically selected in the sequences area of the main window and vice versa.