What is a biplot, and how should I interpret data points in a biplot?

A biplot overlays a score plot and a loadings plot in a single graph. In the biplot view, points are the projected observations (samples); vectors (arrows) are the projected variables. If the data are well-approximated by the first three components, a biplot enables you to visualize high-dimensional data by using a 3D space. You can visualize both the patterns (sample distributions) and the features that driving such patterns.

  • Points that are close to each other in the biplot represent observations with similar values.
  • The cosine of the angle between pairs of vectors indicates correlation between the corresponding variables. Highly correlated variables point in similar directions; uncorrelated variables are nearly perpendicular to each other.
  • The cosine of the angle between a vector and a principal component axis indicates the contribution of the corresponding variable to the principal component: the more parallel to an axis is a vector, the more it contributes only to that PC.

To perform biplot visualization:

  1. Select “Biplot (merged view)” under View options in the top menu bar.

  2. Select omics type, features to be displayed and color of arrows using the dialog

  3. Biplot visualization: each arrow represent a feature, top 5 features based on differential expression analysis from each dataset are displayed here.

More than 2000 genes and 70 taxa were statistically significant in my lists. I selected ten genes and ten taxa. Only five genes and three taxa were displayed.

What are the criteria for deciding how many arrows show up?

Thank you.

By default, it should be the top significant features. Could you share with me your datasets so I can reproduce the issue. Another way is that you can select “Custom” under Feature Selection option and manually enter the taxa or genes to be plotted.


Hi Guangyan,

Thank you very much again for your kind assistance. I tested your suggestion by manually entering the gene names and hitting “highlight” or “reset” (which one is correct? ) Neither button worked for me.

Here are the files used for my analysis. Please remove them after downloading, as usual. These are unpublished data. I appreciate your understanding very much. :pray:

Hi Guangyan,

Although the “advanced options” did not allow me to manually enter the genes/taxa for arrows, I could manually select features from the right panel and show them as arrows in the plot. This is great!

Thank you.