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Figure 14.2 shows the LD plot with the genetic markers plotted in the order that they appear in the spreadsheet and colored according to the LD Correlation. With n markers, the plot has n² elements, making the memory usage and running time of the plot increase quadratically with the number of markers. If you have more than a couple of thousand markers, it may be best to select only a subset of the columns in the spreadsheet at a time for doing LD analysis. Note, that if you run LD analysis in scripting mode, the memory usage is small as the plot does not need to be held in memory – the script just dumps the results to disk. So if you wish to do huge LD computations, it might be better to run them in scripting mode.

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The two drop down menus allow you to plot axes from three choices: -log10P, LD correlation, and D-Prime. Figure 14.3 shows one of the menus opened.

There are several functions to know about:

14.2.1 Stop Calculation/Stop Refresh and Resume Calculation/Resume Refresh

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In Fig. 14.4, the top button (shown saying Refresh) says Stop Calculation only during the initial calculation of the matrix. To stop the calculation, press the Stop Calculation button. Pressing the Stop Calculation button causes the button to change to Resume Calculation. To continue the interrupted computation of the LD matrix click Resume Calculation.The resulting calculation is stored in an internal matrix for faster re-plotting.

After the initial calculation is finished, the button shows Refresh as in Fig. 14.4. If you click the Refresh button, the matrix is recalculated. During the recalculation the button face changes to Stop Refresh. To stop the recalculation, press the Stop Refresh. Pressing the Stop Refresh button causes the button to change to Resume Refresh. Click Resume Refresh to continue the interrupted computation of the LD matrix.

For thousands of markers, machine memory may be insufficient for a full plot, which makes necessary the selective filling in of regions of interest using Fill Mode, explained in Section 14.2.4.

14.2.2 Copy to Clipboard

Clicking on any marker on either axes causes a table to appear in the lower left corner and the <-Copy to Clipboard button to become active. This table is updated whenever the mouse is clicked on the plot or when the arrow keys are used to move from point to point on the plot. An example of the table can be seen in Fig. 14.5 in the Fill Mode section.

To copy the table of numbers at lower left to the clipboard for pasting into other applications, click the <-Copy to Clipboard button.

14.2.3 Plot Visual: Color or Black and White

The drop down menu on the lower left allows you several ways of showing the plot. You can choose:
∙ Multi - color
∙ White - red
∙ Black - white
∙ Blue - red

Whatever colors you choose carry through into any saved BMP files or prints of the LD plot.

14.2.4 Fill Mode

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For larger data sets that are computationally intensive, holding down the Left-click button and dragging the mouse diagonally over a region of a plot creates a rectangle that defines an area to be computed and filled in first before the rest of the overall plot. Once this area is filled in the remainder of the plot will fill in.

Once the plot is created, left-clicking and dragging an area of the plot opens the Haplotype Frequency Viewer window for the haplotypes in the area defined by the mouse drag. The Haplotype Frequency viewer is documented in Section 19.2.

14.2.5 Zoom Mode

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Holding down the Right-click button and dragging the mouse diagonally over a region creates a rectangle that defines an area that opens up an LD Zoom window with a plot of the sub-region just defined by the rectangle. A file tab is created at the bottom of the screen LD Zoom n labeling the zoomed graphic. You can click on the file tab LD Plot of N to return to the main plot, from which different LD Zoom windows can be opened.

If it turns out you do not need the data on the current zoom (tab), you can use the “X” on the lower-right corner of the viewer to delete the zoom, both from the view and from the project itself. (If you do not save the project changes, the action of such a deletion will not be saved and the zoom will be retained.)

14.2.6 Click on Graph

When you click anywhere on the LD plot, a table of statistics is generated in the lower left corner of the window. An example of this can be seen in Fig. 14.5.

14.2.7 Modify Color Scaling

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The color guide at the right of and above the plot (Fig. 14.7) defines the mapping between the colors and the numerical linkage disequilibrium correlation. It is possible to click and drag over a region of the color guide to obtain a narrower window of color (Fig. 14.8). If you shift-click and drag over the scale, the axes will be made symmetric (i.e., use the same LD measure) and have an identical range.

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