Alpha rarefaction plot showing negative faith pd values and different scale bars

When I run alpha rarefaction on my faith_pd alpha diversity values, my y-axis shows negative faith pd values (even though none of my samples contain negative numbers). In addition, when I’m comparing alpha rarefaction plots, my scale bars are different. Is there a way to remove the negative faith pd values on my y-axis and make my scale bars identical? Thank you.

Hey there @Stephanieorch!

Okay, I got a little confused reading your question, but I think this is what I got out of it:

  • None of your faith's pd values are negative.
  • Sometimes the minimum extent of the y-axis scale bar is a negative number, sometimes it isn't.
  • You want to know how to change the minimum extent of the y-axis scale bar.

At the moment, changing the extent isn't possible --- the axis extents are computed automatically using the values currently shown in the plot as a basis for their range. This works well enough, given that the plot is intended for interactive analysis, not for inclusion in a publication. With that said, we have plans to overhaul this viz sometime, and allowing the extents to be customized would be cool. In the meantime you can grab the raw data out of the viz and plug it into your favorite plotting tool!

Hope that helps! :qiime2: :t_rex:

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