Output Graphics and Action Buttons | Genetics | Relationship Matrix

Relationship Matrix
Running this process for the GeneticMarkerExample sample setting generates the tabbed Results window shown below. 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.
The Results window contains the following panes:
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:
Heat Map Results : This tab displays the computed relationship matrix across samples using the JMP Hierarchical Clustering Platform. It is generated when the Plot Relationship Matrix heat map check box is checked. Note : If a Pedigree ID variable was specified on the dialog , no tabbed output is shown.
IBD/IBS Pairs Results : This tab displays a distribution of the number of sample pairs with an Identity by Descent ( IBD ) or Identity by State ( IBS ) value above the threshold specified using the Identity By Descent Threshold option or Identity By State Threshold option, respectively.
PCA 2D Row Scores : This tab, which shows a scatterplot of principal component scores computed on the relationship matrix, is generated when the Perform Principal Components Analysis option is checked. These PCA results are useful to highlight patterns in the relationship matrix.
PCA 3D Row Scores : This tab, which displays a 3-D scatterplot of the first three principal components colored either by the clusters from the Hierarchical heat map or by a specified Color Variable , is generated when the Include 3D plots option is checked.
Scree Plot (Relationship Matrix) : This tab displays the proportion and cumulative variability in the relationship matrix explained by the number of principal components selected.
Output Data
This process generates the following output data sets:
Input Data with IBD SVD Root from Relationship Matrix : This data set contains the original input data set appended with the calculated SVD Root of the Relationship Matrix . This data set is in the format necessary to run the follow-up Q-K Mixed Model process in order to treat the relationship matrix correctly as a random effect . It is created if the Compute the root of the matrix by SVD option is checked. If either the IBS or the Allele Sharing Similarity metric is used instead of IBD , the IBS or AS respectively will be shown in the output data set description.
IBD Relationship Matrix from RelationshipMatrix : This output data set link is generated when either a Pedigree ID variable is specified or the options to Plot Relationship Matrix heat map and Perform Principal Components Analysis are both unchecked and a 0 value is specified for either the Identity By Descent Threshold or the Identity By State Threshold .
For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets .
Launch Follow-up Processes
Q-K Mixed Model : Click Q-K Mixed Model to launch the Q-K Mixed Model process with the input data with appended SVD root matrix (listed in the Output Data Pane above) and the annotation data set (optional) preloaded as input. Note: This follow-up process is available only if the Compute the root of the matrix by SVD option is checked.
Multidimensional Scaling : Click to launch the Multidimensional Scaling process with the relationship matrix output data set preloaded as input. This process enables you to visualize the patterns in the relationship matrix using a dimension reduction technique.
K Matrix Compression : Click to launch the K Matrix Compression process with the relationship matrix output data set and the original input data set preloaded as input. This process compresses the size of the matrix before using it as the random effect in a Q-K Mixed Model analysis.
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.