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  • $\begingroup$ What did you plot in the PCA score plot? $\endgroup$ Commented Jan 28 at 10:53
  • $\begingroup$ The PCA score plot I visualized shows the data projected onto the first two principal components (PC1 and PC2). $\endgroup$ Commented Jan 28 at 11:48
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    $\begingroup$ PCA does not have a target variable. The PCA score plot (as described in your comment) is not intended to find separation on some other variable. Also, your score plot showed only two PCs; you didn't tell us how many PCs you used as features, but if it was more than 2, that isn't captured in the plot. $\endgroup$ Commented Jan 28 at 12:02
  • $\begingroup$ You can, of course, use the PCs to do classification (as you did). $\endgroup$ Commented Jan 28 at 12:03
  • $\begingroup$ How many PCs did you use as features? All of them or just the first two from your visualization? Also, how do you assess the accuracy to be high? Do you, for instance, calculate on some holdout data? If so, how do you calculate the features for the holdout data? $\endgroup$ Commented Jan 28 at 12:14