Displays the results from a linkage disequilibrium analysis.
After selecting the desired result from the Data Tree, choose Results -> LD Plot
The graph that is generated displays LD between pairs of sites calculated with the analysis step. The black diagonal represents LD between each site and itself. The default setting graphs r2 in the upper right and p-values in the lower left. This default can be modified by clicking on the buttons in the lower left. The left side of the graph contains a text description with the Chromosome and the Site name. At the bottom of the graph is a display of the position of each site along the chromosome. This display can be hidden by deselecting the “Schematic” check box. Legends that describe the color scheme appear on the right hand side of the graph. The number of sites displayed can be selected by entering a number in the white box in the upper right corner or by moving the sliding bar next to it. To move through the graph use the sliding bars on the right and bottom. The red box in the small white window in the upper left corner will show what portion of the graph is displayed. To move only around the diagonal select the “Lock Y Axis to X” check box (recommended when visualizing a LD by sliding window analysis).
LD plots can be saved in several formats. The Save button will save the area of the graph shown in the screen, while the Save All button will save the entire graph.