When use metaboanalyst for pricinpal component analysis, a 2D pca socre plot with optional 95% confidence region can be obtained, while the metaboanalyst provide some options for customizing the plot, I would like to obtain the raw data of the plot, i.e., the coordinates of each point as well as the 95% confidence level, so that i can plot the PCA data elsewhere and do further analysis and custmomize the plot

Take a look at the “**pca_scores.csv**” in the download page.

Thank you, your reply is indeed helpful.

The remaining issue is that the pca_scores.csv file does not contain the raw data of the 95% confidence level, then how can I get the raw data of the confidence level, i.e., the coordinates of the ellipse of each class, or how can I calculate the confidence level by myself?

You can use the R package “ggplot2” to add this feature (or search other programs online). We do not even have coordinates for this ellipse saved anywhere - it is calculated by the graphics software.