What's the purpose of add a axis with continuous value in qiime2 pcoa plot?

I do not know the optional choice in qiime empror plot: custom-axis, what information can we know if i conduct this step?

Hi @jidong_zhao,
A custom axis is useful if you want to examine how PCoA changes across a continuous metadata variable. For example, you could see how ordinations change across gradients of pH, longitude/latitude, or time.

As an aside, methods in q2-longitudinal are also useful for this, particularly when time is the continuous variable. For example, volatility plots can be used to plot how PC coordinates change over a continuous gradient. The advantage of using emperor is that you can view 2 PCs against the custom axis and have interactive control over coloring/formatting. The advantage of q2-longitudinal’s volatility visualizer is that you can examine individuals’ coordinates changes across the gradient (by using the spaghetti parameter to generate what we call a “spaghetti plot”). :spaghetti: :smile:

I hope that helps!

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