Linkage Order Results

The Linkage Order Results tab is shown below:

The Linkage Order Results tab contains the following elements:

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One plot of computed genetic distance by linkage group

This plot displays a visual representation of the genetic linkage map. The computed genetic distance is plotted on the y-axis with the Linkage Group Variable on the x-axis. For each linkage group, the markers are displayed as points in the optimized order determined by the Order Algorithm.

NoteThe y-axis is in opposite order from a typical plot, starting at 0 at the top of the plot going to the maximum computed genetic distance across all linkage groups.

The markers are colored by a specified input Color Variable. This can be useful to color based on other known consensus map positions for map comparison. If no variable is specified, points are colored either by Linkage Group when running Map Order Optimization or by a summarized metric of residuals from MDS if Multidimensional Scaling is used for marker order.

Note: Map Order Optimization is the preferred (superior) ordering algorithm.

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One JMP Data Filter

The data filter to the right of the map order plot can be used to filter the view to show markers that have large genetic distance gaps between them (or alternatively recombination frequencies). This can be helpful to decide whether the groups should be further broken into smaller groups based on a threshold using the Break linkage groups between markers with large ordered distances parameter and related options. You can also add additional filtering variables using the AND or OR buttons with the data filter.

See JMP Data Filter help for more information.

This tab is useful to visualize the results of the marker ordering and the complete genetic distance map across markers. Note that if you choose to use the Reverse Linkage Group Marker Orders action button, this plot will be refreshed with the new positioning of markers.