Barplots grouped by feature, how does the math work?

[Nicholas_Bokulich]

@Kotryna

Could metadata be a problem?

Certainly could be, but you'd probably notice any obvious issues by now.

@Kotryna

But let’s say those 3 outweighs the others and the result is true for sum mode , but what about median and mean?

Now that I think about it, sum, mean, and median would all most likely be impacted by uneven sampling. This is the most likely cause of the issue you are seeing.

@Kotryna

When I look at the rarefying curves, I’d not say that those 3 samples have much more sequences; all those 10 samples that I have make a nice ‘gradient’

don't go off the rarefaction curve — look at the total reads per sample.

But even sampling (with the qiime feature-table rarefy action) would be one way to correct this for the purposes of making a barplot. This issue is pretty similar to this topic:

TAXA barplot using relative frequency (not absolute frequency)

Hello, I want to obtain a taxa barplot using relative abundance data. I see that Taxa barplot plugin uses a FeatureTable[Frequency], but I wonder if it could use a FeatureTable[relative frequency] instead. The problem with FeatureTable[Frequency] is that it does not normalize taxa abundance by the total number or reads of each sample. For instance: S. aureus sample 1= 1000; Sample 2= 100; Sample 3= 2000; …

If you want to positively confirm, I'd say export the data and sum those features by hand (first collapse by taxonomy to replicate what barplot is doing)

I hope that helps!