Output | Genetics | Linkage Map Order

Linkage Map Order
Running this process for the BackCross_Example sample setting generates the tabbed Results window shown below. Refer to the Linkage Map Order process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on, that facilitate your analysis.
Tab Viewer
This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.
The following tabs are generated by this process:
Linkage Order Results: This tab displays a plot of the genetic distance as calculated based on the optimized/estimated marker order for each linkage group. Genetic distance (either Kosambi or Haldane) is plotted on the y-axis against linkage group on the x-axis.
Genotype Color Plots: This tab displays a cell plot for each linkage group colored by the marker genotypes. This plot is useful to visually evaluate the marker order and can also detect potential genotyping errors in the data. This tab only is displayed if a Genotype Data Set is specified and the Display marker genotype cell color plots check box option is checked.
MDS Residual Plots: This tab, not shown by default, will be available only if Multidimensional Scaling is chosen as the Order Algorithm. It displays plots of the residuals from the MDS model for each linkage group. In general, this method gives only a rough estimation of map order and should be used only if Map Order Optimization cannot be completed or if the linkage groups are very small and well formed.
SAS Output: This tab displays the SAS output numerical results and history of the Map Order algorithm.
The map order optimization algorithm runs the OPTMODEL Procedure in SAS/OR to use a traveling salesman problem approach to determine optimal marker order. The results of the procedure are shown in this tab. If MDS was used for the order algorithm, results from the MDS Procedure in SAS/STAT would be shown. The Map Order Optimization is a superior algorithm for determining order and should be used when feasible.
Drill Downs
Action buttons provide you with an easy way to drill down into your data. The following action buttons are generated by this process:
Linkage Group X: One or more buttons (one for each linkage group) in the Launch Interactive Order and Recombination Plots outline box. Click Linkage Group 1 to launch a triangle plot view (shown below) of the markers in the computed order for the specified linkage group.
The colored triangle plot corresponds to pairwise values of recombination frequency for the markers in the linkage group. The genetic distance and marker labels are plotted at the top of the plot along the x-axis (genetic distance in cM). You can annotate this plot to add blocks of regions where there might be a significant QTL signal or other known information.
Reverse Linkage Group Marker Orders: Click Reverse Linkage Group Marker Orders to reverse the order either for selected groups or all linkage groups, so that the marker that was originally placed first (at 0 genetic distance) becomes the last marker and vice versa. This feature is useful when trying to match marker orders to known consensus orders or chromosomal order.
Launch Follow-up Processes
Linkage Map Viewer: Click this button to launch the Linkage Map Viewer process with the generated output data set from the Linkage Map Order process (data set with suffix _lmo) preloaded as input. This process enables you to visualize the computed linkage map using a custom JMP graphic.
Subset and Reorder Genetic Data: Click to launch and run the Subset and Reorder Genetic Data process using the generated output data set from the Linkage Map Order process and the Genotype Data Set (if specified) preloaded as input. You must run this process to reorder the original genotype data set to match the computed genetic linkage map annotation for further QTL analysis processes.
Click View Data to reveal the underlying data table associated with the current tab.
Click Reopen Dialog to reopen the completed process dialog used to generate this output.
Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.
Click Close All to close all graphics windows and underlying data sets associated with the output.