alpha-rarefaction output

[larusnz]

When I view the QIIME 2 output file “alpha-rarefaction.qzv” using QIIME 2 View I can obtain a plot of observed OTUs that looks as expected using the visualisation tab.

I then click on the ‘Details’ tab and download a copy of the data underpinning this plot.

However, when I examine the data closely I cannot reconcile the values in the table with those visualised in the plot. For example, a particular site is plotted with a mean observed OTUs that appears to be ~450 (reading off the y-axis) at sequencing depth of 4000. When I go to the data table and look at the data for this site across the depth-4000_iter_n columns the mean is 548. It seems that all the values in the plot are slightly offset from the mean values I obtain from the table.

My question is, what exactly is being plotted as the centre of the box plots along the rarefaction curves? Is it the mean, or some other value obtained from the data?

[Mehrbod_Estaki]

Hi @larusnz,
Those are IQR boxplots, so the middle line would be the median, which may be different than the mean. Does that match with what you see in the table?

[larusnz1 (Jamie)]

Thank you for the clarification - that makes a lot more sense!