Alpha-rarefaction plot


(Luca) #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).

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


(Matthew Ryan Dillon) #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:


(Luca) #3

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

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


(Matthew Ryan Dillon) #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.


(Luca) #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


(Matthew Ryan Dillon) #6

:smile:

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

Thanks!


(system) closed #7

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