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. Author manuscript; available in PMC: 2020 Sep 17.
Published in final edited form as: Methods Mol Biol. 2017;1488:75–120. doi: 10.1007/978-1-4939-6427-7_4

Fig. 12.

Fig. 12

Principal component analysis (PCA). As part of the matrix tool, a PCA is performed on the selected traits. The Scree Plot (left panel) plots each principal component (PC) based on the amount of variance each PC or factor explains. The Factor Loadings Plot displays the loading (the correlation) between each treat (the measured variable) and the factor or PC (latent variable). Each PC can be treated as a trait. If selected the same basic functions and tools for individual trait analysis can be used for the PC. QTL mapping is shown for PC1 in the top right panel. Interval mapping does not suggest strong genetic control originating from a single locus for PC1