Miscolored PCA and PLS-DA Plots


I’ve been noticing issues with the colors in my PLS-DA plots over the past week. Although the sample colors (dots) are correct, the 95% confidence regions are miscolored. I’ve tried altering the colors manually, but it doesn’t fix this issue. This problem seems to occur with about half of the data sets I upload.

I’ve attached an image showing what this looks like. Could you please look into this?


Thank you so much.

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I had the same problem! I found that if you go straight away to the graph you want and change the color there first, it works.

For example for me I changed the colors at the volcano plot, and the colors of my PCA were mismatched. But I reloaded the data and changed the colors at the PCA tab, and everything was fine

Hope that helps

I am having this problem as well. Although for me the 95% confidence regions are correctly colored and the sample dots are swapped. I have tried everything from uploading the data again, to changing the color settings in PLS-DA, to using MetaboAnalyst in a different browser (Chrome vs Microsoft Edge). Nothing has fixed this issue for me. Any advice would be appreciated, this issue has been happening for a few weeks and I would really like to get my plots put together.

I am closing this topic due to lack of details. You can open a new post following our post guideline