PCA Plot componenets

Question

[####]

PCA PLOT with 2 components is better over 3 components or PLOT with 3 components is better over 2 and why ?

[russhh]

2 components are easier to plot; 3 components might tell you more about the structure of your data. This is a bit of a subjective question for Biostars though

[Benn]

This totally depends on your data, i.e., how much percentage of variation is represented in each PC. Usually you see that one factor is explained in one direction (PC), and another factor in the other direction. For example, if you compare diseased versus healthy persons, this difference might be shown in PC1 (healthy to the left, diseased to the right), and gender might be explained in the PC2 direction (women up, and men down). If there is a clear third factor which is present in PC3, 3D plot might be useful. Depends on how complex your dataset is.

Answer 1

[Mahdiar Sadeghi]

Whatever that presents the data better. 3D plots might be confusing depending on your data. In general, 2 component plots are good for presentation and easy to digest. You can add the 3rd component by color scale.