How to plot Rarefaction curve showing standard deviation in the curve and colored by groups or metadata

[DPC7]

Hi I am using phyloseq and vegan to plot rarefaction graph. I only succeed to plot a curve like this:

But, I want the x axis to be number of samples, and curves to be plotted on the basis of metadata information (e.g. sample_type (control, test), etc.). Exactly like the curve in this article page .

Can anyone please help me out?

Thanks
dpc

[jarioksa]

If you want to show the accumulation by sampling units, you should use species accumulation curves instead of rarefaction (rarefaction is within sampling units, species accumulation is among sampling units). Check function specaccum in vegan. The default method = "exact" is similar to the rarefaction method, and argument subset can be used to select a subset of sampling units. Two accumulations can be plotted by setting argument add = TRUE for the second plot command.

[DPC7]

Thanks a

If you want to show the accumulation by sampling units, you should use species accumulation curves instead of rarefaction (rarefaction is within sampling units, species accumulation is among sampling units). Check function specaccum in vegan. The default method = "exact" is similar to the rarefaction method, and argument subset can be used to select a subset of sampling units. Two accumulations can be plotted by setting argument add = TRUE for the second plot command.

Thanks a lot @jarioksa for helping me out. I have followed this tutorial and able to generate graph as per the tutorial. BUT, how can I see two different curves for control and test sample groups in my metadata?

DC7

[jarioksa]

I think I told that in my message. Look at the last sentence.

[DPC7]

Thanks sir... yes, I have done it.... I didn't understand that at very first....

Thanks a lot for helping me out...

DC7

[DPC7]

If you want to show the accumulation by sampling units, you should use species accumulation curves instead of rarefaction (rarefaction is within sampling units, species accumulation is among sampling units). Check function specaccum in vegan. The default method = "exact" is similar to the rarefaction method, and argument subset can be used to select a subset of sampling units. Two accumulations can be plotted by setting argument add = TRUE for the second plot command.

Sir @jarioksa , then why they captioned as "rarefaction"? They did not get a curve for each of the samples.