3.16. Expression map

The "Expression map" dialog box displays the gene expression matrix. This dialog box is accessed by clicking the Analysis>Expression map main menu command. When the map is being loaded, you can see the "Drawing diagram" information box (Fig 3.16.1) that will disappear after the loading is complete.


Figure 3.16.1 Information box.

The "Expression map" dialog box has the following elements (Fig. 3.16.2):


Figure 3.16.2 "Expression map" dialog box
1. Main (system) menu. 2. Toolbar. 3. A pane with column names 4. A pane with row names. 5. Matrix view area. 6. Status bar.

The main menu of this dialog box has the following menus:

The Toolbar has the following buttons:

("Column name") shows the Column names pane.
("Row name") shows the Row names pane.
("Fit mode") resizes the image to fit as closely as possible within the current view area frame.

The Column names pane shows the names of matrix columns. To display the pane, click .

The Rows names pane shows the names of matrix rows. To display the pane, click .

The View area displays the expression matrix map.

The Status bar displays information about the expression matrix cell you are pointing to with your mouse pointer: gene number, gene name, field number, field name, and the field value.

3.16.1. "Pattern setup" dialog box

3.16.1. In the "Pattern setup" dialog box (Fig. 3.16.1.1), you can set up the parameters of the expression matrix image. To open this dialog box, click the Image>Image setup command. The "Pattern setup" dialog box has the following elements:

3.16.1.1. The "Palette type" list that includes the following options:

    3.16.1.1.1 "White(min)->Colormax" -the color of matrix cells changes from white to the most saturated color defined in pane 3.16.1.4.
    3.16.1.1.2. "Black(min)->Colormax" -the color of matrix cells changes from black to the most saturated color defined in pane 3.16.1.4.
    3.16.1.1.3. "Colormin->White->Colormax" -the color of matrix cells changes from the least saturated color defined in pane 3.16.1.5 to the most saturated color defined in pane 3.16.1.4. The intermediate color is white.
    3.16.1.1.4 "Colormin->Black->Colormax"- the color of matrix cells changes from the least saturated color defined in pane 3.16.1.5 to the most saturated color defined in pane 3.16.1.4. The intermediate color is black.
    3.16.1.1.5. "Geographic map colors" - the pallet of geographic map colors.

3.16.1.2. The "Range type" list that has the following options:

    3.16.1.2.1. "Value intervals" - the color range of a matrix element depends on the gene expression value in the current tissue.
    3.16.1.2.2. "Rank percent intervals" - the color range of a matrix element depends on the rank of the gene expression value in the current tissue.

3.16.1.3. In the "Max. value color" pane, you can set the color for the maximum value. This option is available for palettes 3.16.1.1.1, 3.16.1.1.2, 3.16.1.1.3, and 3.16.1.1.4. Click the "Color" button to open the "Select color" dialog box where you can select the desired color. The color you selected is shown in the "Preview" pane.

3.16.1.4. In the "Min. value color" pane, you can set the color for the minimum value. This option is available for palettes 3.16.1.1.3 and 3.16.1.1.4. Click the "Color" button to open the "Select color" dialog box where you can select the desired color. The color you selected is shown in the "Preview" pane.

Control buttons:


Figure 3.16.1.1 "Pattern setup" dialog box.
1. List of palettes. 2. List of range types. 3. The "Field specific ranges" checkbox. 4. The Maximum value color pane. 5. The Minimum value color dialog box. 6. The "OK" button that closes the dialog box and applies changes. 7. The "Cancel" button that closes the dialog box and cancels changes.

3.16.2. "Image options" dialog box

In the "Image options" dialog box (Fig. 3.16.2.1), you can configure the general image parameters. The dialog box has four tabs:

"Common & Borders" tab (Fig. 3.16.2.1) sets the general image options:

The "Common" pane has the following checkboxes:

The "Borders" pane has the following options for the cell borders and image background:

In the "Border width" field, you can define the border width in pixels.

Click the "Color" button to open the "Select color" dialog box and select the border color. The current border color is displayed in the "Border" view pane.

Click the "Color" button to open the "Select color" dialog box and select the background color. The current background color is displayed in the "Background" view pane.


Figure 3.16.2.1 "Image options" dialog box. "Common & Borders" tab.
1. The "Fit mode" checkbox. 2. Visible row headers mode. 3. Visible column headers mode. 4. Visible borders mode. 5. The field for adjusting the border width. 6. The pane for selecting the border color. 7. The pane for selecting the background color. 8. The "OK" button that closes the dialog box and applies changes. 9. The "Apply" button that applies changes and leaves the dialog box open. 10. The "Cancel" button that closes the dialog box and cancels changes.

The "Sizes" tab (Fig. 3.16.2.2) sets the matrix cell sizes:


Figure 3.16.2.2 "Image options" dialog box. "Sizes" tab.
1. The pane for setting custom sizes of matrix cells. 2. The pane for setting maximum sizes for "Fit Mode". 3. The pane for setting minimum sizes for "Fit Mode". 4. The "OK" button that closes the dialog box and applies changes. 5. The "Apply" button that applies changes and leaves the dialog box open. 6. The "Cancel" button that closes the dialog box and cancels changes.

The "Row Headers" tab (Fig. 3.16.2.3) has the following options for row headers:

The "Short Headers" checkbox. If this box is checked, only short names are displayed as row headers.

In the "Number of Visible Characters" field, you can specify the maximum number of characters in short names.

In the "Interval" field, you can specify the space between headers (in pixels). This field is active when the "Fit Mode" checkbox is unchecked.

In the "Row Width" field, specify the width of row headers.

In the "Alignment" list, select the alignment type for the cell contents:

"Left" - to left margin
"Center" - centered
"Right" - to right margin

Click the "Color" button to open the "Select color" dialog box (see section 3.18) and select a new color for row names.

Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a new font for row names.

The "Preview" pane shows the selected font, color and alignment of row names.


Figure 3.16.2.3 "Image options" dialog box. "Row Headers" tab.
1. Short headers mode. 2. Number of characters in short names. 3. Space between row headers. 4. Alignment types for cell contents. 5. The button that opens the "Select color" dialog box from where to adjust colors for row headers. 6. The button that opens the "Select font" dialog box from where to customize fonts for row headers. 7. The "Row width" field. 8. The "Preview" pane. 9. The "OK" button that closes the dialog box and applies changes. 10. The "Apply" button that applies changes and leaves the dialog box open. 11. The "Cancel" button that closes the dialog box and cancels changes.

The "Column Headers" tab (Fig.3.16.2.4) has the following options for column headers:

The "Short Headers" checkbox. If this box is checked, only short names are displayed as column headers.

In the "Number of Visible Characters" field, you can specify the maximum number of characters in short names.

In the "Interval" field, you can specify the space between headers (in pixels). This field is active when the "Fit Mode" checkbox is unchecked.

In the "Column Height" field, specify the height of column headers.

In the "Alignment" list, select the alignment type for the cell contents:

"Top" - to the top of the cell
"Middle" - to the middle of the cell
"Bottom" - to the bottom of the cell

Click the "Color" button to open the "Select color" dialog box (see section 3.18) and select a new color for column names.

Click the "Font" button to open the "Select font" dialog box (see section 3.19) and select a new font for row names.

The "Preview" pane shows the selected font, color and alignment of row names.


Figure 3.16.2.4 "Image options" dialog box. "Column Headers" tab.
1. Short headers mode. 2. Number of characters in short names. 3. Space between column headers. 4. Alignment types for cell contents. 5. The button that opens the "Select color" dialog box from where to adjust colors for column headers. 6. The button that opens the "Select font" dialog box from where to customize fonts for column headers. 7. The "Column height" field. 8. The "Preview" pane. 9. The "OK" button that closes the dialog box and applies changes. 10. The "Apply" button that applies changes and leaves the dialog box open. 11. The "Cancel" button that closes the dialog box and cancels changes.

Note. The "OK" button that closes the dialog box and applies changes. The "Apply" button that applies changes and leaves the dialog box open. The "Cancel" button that closes the dialog box and cancels changes.