Scale axis in Emperor

Is there a way of choosing how to scale the axis in Emperor? In Qiime 1 we have the option of scaling coordinates by percent explained.

The reason I am asking this is because I have a plot in which PC2 explains 19% and PC1 explains 43% but regardless of which axis I plot PC2, it is always twice as large as PC1.

Thank you!

Hi @ErikaGanda, pinging @yoshiki to see if he has any thoughts on this.

Thanks @thermokarst! I will wait on any suggestions.


AFAIK that feature is still in the works in the developer’s version of Emperor so at this point the easiest will be to use the old version. Just note that the PCoA files from QIIME2 are not compatible with QIIME1. Thus, the shortest path is to take your distance file and run in QIIME1.

Hope this helps.


@antgonza is right, this is currently still under development.

Do you mean that the length of PC1 is always smaller than the length of PC2? Or what exactly do you mean by this?

The length of PC2 is larger than PC1, regardless of it explaining less than PC1.

The images are below.

Thank you!

Thanks, out of curiosity what metric are you using?

Weighted Unifrac. I am plotting the weighted-unifrac-emperor.qzv

Thanks, to the best of my knowledge it should be fine that one axis is longer than the other, so I wouldn’t worry about that too much. We plan to add the functionality to scale axes soon, but don’t really have a specific ETA.

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Thank you very much!