Contents - Index
Four questions before trying to interpret a biplot
When a biplot is generated, the following questions must be asked before trying to interpret it:
This determines what questions can be asked of the biplot and what cannot. In this biplot, the model is based on Scaling = 0 (original data not divided by anything) and Centering = 2 (tester-centered). And, the data was not transformed (Transform = 0). Therefore, this is a "GGE biplot" without scaling. It has all the interpretations of a GGE biplot.
In Depth: Various biplots for analyzing a genotype-by-environment table.
Even More: All possible biplots based on a single two-way table
This is crucial if the purpose is to visualize the relationships among entries or that among testers. In the above biplot, SVP = 1 (entry-focused singular value partitioning). It is therefore more appropriate for entry evaluation but not so for tester evaluation. However, the choice of SVP does not affect the interpretation of entry by tester interactions.
The higher the goodness of fit of the biplot, the more confident the researcher is about the interpretation based on the biplot. If only a small portion of the variation is explained, the pattern in the data is either complicated or there is no discernible pattern at all. The above biplot explained 89% of the tester-centered data (G+GE), not of the original data.
In Depth: How many PC's are required to fully explore the data
In Depth: What if two PC's are not sufficient for displaying the two-way table
If the axes are not drawn to scale, the relationships among the entries and testers are distorted, which can be misleading. A biplot generated by GGEbiplot is always drawn to scale. However, watch out when reading journal papers and see if a biplot is stretched to fit the space. If so, the biplot may be misleading.
All these pieces of information are explicitly indicated on the top-left corner of the biplot:
1) Goodness of fit: PC1= 63%, PC2 = 26%, Total = 89%;
2) Data transformation method: Transformation = 0;
3) Data Scaling method: Scaling = 0;
4) Data Centering method: Centering = 2;
5) Singular value partitioning: SVP = 1; and
6) Drawn to scale: It is drawn to scale, which is always true in biplots generated by GGEbiplot.