When creating a PLSDA or sPLSDA plot, the colour for the data points and the 95% confidence interval get mismatched. I think there may be a tiny bug in there somewhere. The colour plotting works fine for PCA charts
This was done by using Statistical Analysis (One Factor). I uploaded LC/MS data, peak intensities, samples in unpair columns.
Data was Not filtered, normalized by sum, log transformed, and auto scaled. Colour for the different groups was changed at the volcano plot tab, and updated again at the PCA tab. By the time I got to PLSDA the colors were mismatched.
However, if you change the colors at the PLSDA tab first, everything is fine and nothing is mismatched. But sometimes it will just glitch and mismatch the colors