Alpha-rarefaction plot

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1

Hi all,
question on a alpha-rarefaction plot I got, for which I'm not sure they may be something wrong in my dataset (or more likely my metadata file).

rarefaction
rarefaction3572×1376 256 KB

How is possible that the diversity goes up, than go down again, while increasing the sequencing depth?
Can anyone help to find give a reasonable explanation, please?

Thanks
Luca

2

There should be a sample-count plot below the diversity curve - what does that plot look like? Would you be able to attach the QZV for us? If not, a screenshot of the missing plot would be great --- thanks! :t_rex: :qiime2:

3

Hi Thermokarst,
thanks for your help.
The count plot is the following, and it look normal to me.

SampleCount
SampleCount3216×1378 169 KB

So, I'm not sure why the Shannon metric show the picking in the middle.
I would not expect that, or is quite normal from your point of view?

Thanks
Luca

4

The V metadata group has very few samples in it (looks like it starts with 3) - at around 7000, you lose a sample, which is when the first huge jump in diversity happens. Then, at around 13000 you lose another sample — the jump happens again (opposite direction this time). I would suggest plotting the feature-table summarize viz, with your metadata, then look at the interactive rarefaction plot, for this particular metadata column ---- then, figure out which samples are in that group (V), and which one is lost first, second, etc.

I would say that this doesn’t surprise me, given how few samples are in that group. This also indicates you have a bit of variability within that group, too, which might be interesting when you get to beta diversity.

5

Thank you!
Yes, V is a group with not many samples, and make sense there is high variability in the group.
Just in my mind I though the diversity as the upper limit for the group and could not think how can increase if a sample is lost. I will rethink this from now on.

PS I tried to send in private the qzv but is to large for the system.

Luca

6

:smile:

Usually if that is the case you will need to upload the file somewhere else and share a direct-download link.

Thanks!

7

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